Cell lines and host nucleic acid sequences related to infectious disease

ABSTRACT

Host nucleic acids and host proteins that participate in viral infection, such as human immunodeficiency virus (HIV), influenza A, and Ebola virus, have been identified. Interfering with or disrupting the interaction between a host nucleic acid or host protein and a virus or viral protein confers an inhibition of or resistance to infection. Thus, interfering with such an interaction in a host subject can confer a therapeutic or prophylactic effect against a virus. The sequences identified can be used to identify agents that reduce or inhibit viral infection.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Nos.60/427,464 filed Nov. 18, 2002 and 60/482,604 filed Jun. 25, 2003, bothherein incorporated by reference.

FIELD

The present disclosure relates to host nucleic acid sequences, andproteins encoded by these sequences, that are involved in viralinfection or are otherwise associated with the life cycle of a virus.Decreasing or inhibiting the interaction of these host sequences with aviral sequence can be used to decrease or inhibit infection by thevirus.

BACKGROUND

Infectious diseases affect the health of people and animals around theworld, causing serious illness and death. Public health efforts havefocused on behavioral modification and other public health efforts toreduce the incidences of infection, while treatment regimens for thesediseases have focused on pharmaceuticals, such as antibiotics andanti-viral medications. However, educating people about modifyingbehavior can be difficult, and that approach alone rarely cansignificantly diminish the incidence of infection. Furthermore,modifying the behavior of domestic or wild animals would not result indiminished infections. Stopping the spread of infections in an animalpopulation typically involves wholesale slaughter. Few vaccines areavailable or wholly effective, and they tend to be specific forparticular conditions.

The rate of HIV (human immunodeficiency virus) infection is increasing.HIV and its associated acquired immune deficiency syndrome (AIDS)accounted for approximately 5% of all deaths in the United States in theyear 2000, while over 313,000 persons were reported to be living withASS in that same year. Centers for Disease Control and Prevention,HIV/AIDS Surveillance Supplemental Report, 8(1):1-22 (2002). Theseincreasing infection rates have occurred, even though the mode of HIVinfection has been known for almost 20 years, and educational programsaround the world have promoted behavioral modifications meant to reduceHIV infection. Incidence and death rates due to HIV disease have beendecreasing since the mid-90's, in part due to aggressive antiviraltherapies, which frequently have toxic side effects and strict dosageschedules. However, even with treatment, the patient is not cured of thedisease, and to date, no effective vaccine therapy has been found.

In other diseases, such as infection by the Ebola virus, not only aretreatments limited, but containment or prevention of infections isdifficult because the life cycle of the virus is not well known. Thenatural reservoir for the Ebola virus, that is the place or populationin nature where the virus resides between human outbreaks, has not yetbeen identified.

Additionally, different viral strains can rapidly evolve in response todrug usage, producing drug-resistant strains. For example, strains ofthe influenza virus resistant to amantadine and rimantadine haverecently arisen. A recent study of 80 newly-infected people conducted bythe AIDS Research Center at Rockefeller University in New York, foundthat as many as 16.3% of these individuals had strains of HIV associatedwith resistance to some treatments, and 3.8% appeared to be resistant toseveral currently available anti-HIV drugs. Thus, a need exists foralternative treatments for infectious disease and methods of designingnew drugs to combat infectious disease.

SUMMARY

Several host nucleic acid sequences involved in viral infection havebeen identified using gene trap methods. The identification of thesehost sequences and their encoded products permits the identification ofsequences that can be targeted for therapeutic intervention.

The disclosed host sequences (including the target sequences associatedwith SEQ ID NOS: 1-227, 229, and 231, and the proteins encoded thereby(such as SEQ ID NOS: 228, 230, and 232), as well as variants, fusions,and fragments thereof that retain the appropriate biological activity)can mediate infection, and in some examples these host nucleic acids arerequired for infection. For example, the host nucleic acid can encode acellular receptor or ligand or a fragment thereof that is recognized bya virus, such as the T-cell V-D-J beta 2.1 chain. In another example,the host nucleic acid encodes an enzyme that mediates viral infection,such as the β-chimerin rho-GTPase (referred to herein as β-chimerin). Inanother example, the host nucleic acid encodes a Ras oncogene familymember such as Rab9. It is demonstrated herein that Rab9 is a hostprotein involved in infection by pathogens (such as viruses andbacteria) that use similar pathways for morphogenesis of infectiousparticles. In particular examples, Rab9 is involved in infection bypathogens (such as viruses and bacteria) that utilize lipid rafts. Thus,for example, interfering with the interaction between the disclosed hostproteins and a viral or pathogen protein, for example by disrupting theexpression of the host nucleic acid within a host cell, or byadministering an agent that decreases binding between a host protein anda viral protein, can inhibit, or even prevent, infection of that hostcell by the associated virus. Moreover, the identification of particularhost enzymes or other host proteins involved in infection provides amethod for developing new therapies targeted at inhibiting infection, atthe protein or nucleic acid level.

In some examples, the nucleic acid itself mediates viral infection. Forexample, the nucleotide sequence of a host nucleic acid in the hostgenome can be recognized by the virus during integration of the viralgenome into the host genome. The identification of nucleic acidsequences that are involved in the pathogenesis of infection thereforeprovides an important tool for interfering with infection.

This genomics-based discovery of nucleic acids and proteins involved in,or even required for, infection provides a new paradigm for identifyingand validating various aspects of infectious disease, includingassessing individual or population resistance to infection and findingnovel diagnostic and drug targets for infectious disease and alteringthe nucleotide sequence of the host nucleic acid.

Based on the identification of several host nucleic acid and proteinsequences involved in viral infection, provided herein are methods fordecreasing infection of a host cell by a virus, such as HIV, Ebola, orinfluenza A, or treating such a viral infection, by interfering with theactivity or expression of one or more host proteins shown in Table 1(including the target sequences associated with any of SEQ ID NOS: SEQID NOS: 1-232, as well as variants, fragments, and fusions thereof),such as at least two host proteins, or at least three host proteins.Also provided are methods for identifying agents that can decrease viralinfection of a host cell, such as infection by HIV, Ebola, or influenzaA. In addition, cells and non-human mammals are provided that havedecreased susceptibility to viral infection, such as HIV, Ebola, orinfluenza A infection.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a schematic illustration of the U3neoSV1 retroviral vector,which is capable of isolating the nucleic acids described herein usingthe gene-trap method.

FIG. 2 is a schematic illustration of the gene-trap method.

FIG. 3 is a schematic illustration of one method of identifying hostgenes described herein.

FIG. 4 is a flow chart illustrating a method for isolating cellsresistant to HIV infection, including HIV-1 and HIV-2 infection.

FIG. 5 is a bar graph showing the relative amount of p24 in HIV-infectedcells in the presence of various siRNAs. CHN (β-chimerin); KOX (similarto KOX4 (LOC131880) and LOC166140); RBB (retinoblastoma binding protein1); RAB (Rab9); KIAA1259; F3 (tissue factor 3; thromboplastin); AXL (AXLreceptor tyrosine kinase); Msleb (mammalian selenium binding protein).

FIG. 6 is a schematic drawing showing a model of Rab9 involvement inlipid raft formation.

SEQUENCE LISTING

The nucleotide sequences of the nucleic acids described herein are shownusing standard letter abbreviations for nucleotide bases, and threeletter code for amino acids. Only one strand of each nucleic acidsequence is shown, but the complementary strand is understood asincluded by any reference to the displayed strand. Additionally, thenucleic acid sequences shown in SEQ ID NOS: 1-226 inherently disclosethe corresponding polypeptide sequences of coding sequences (resultingtranslations of the nucleotide sequences), even when those polypeptidesequences are not explicitly provided herein.

SEQ ID NO: 1 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 18E8,entire insert. The human homolog is the (−) strand of GenBank AccessionNo. NG_(—)001333.1, T-ell receptor V beta chain (T-cell receptor beta).Further information on the T-cell receptor V beta chain can be found inWO 01/23409, WO 01/55302, WO 01/57182, and WO 01/94629.

SEQ ID NO: 2 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 18BA,distal end. The human homolog is the (−) strand of GenBank Accession No.AC 104597.3, T-cell receptor V beta chain.

SEQ ID NO: 3 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 18BA,proximal end. The human homolog is the (+) strand of GenBank AccessionNo. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 4 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 18BE,distal end. The human homolog is the (+) strand of GenBank Accession No.AC00616.7, T-cell receptor beta.

SEQ ID NO: 5 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 18BE,middle of insert. The human homolog is the (−) strand of GenBankAccession No. AC104597.3, T-cell receptor beta.

SEQ ID NO: 6 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 18BE,proximal end. The human homolog is the (+) strand of GenBank AccessionNo. NG_(—)001333.1, T-ell receptor beta.

SEQ ID NO: 7 is a nucleic acid sequence associated with viral, such asHIV, infection which corresponds to the sequence identified asNucleotide Sequence 18E6, proximal end. The human homolog is the (−)strand of GenBank Accession No. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 8 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E21,proximal end The human homolog is the (+) strand of GenBank AccessionNo. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 9 is a nucleic acid sequence associated with viral, such asHIV, infection which corresponds to the sequence identified asNucleotide Sequence 2E22, proximal end. The human homolog is the (−)strand of GenBank Accession No. AC099395.2, T-cell receptor beta.

SEQ ID NO: 10 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2B13,proximal end. The human homolog is the (−) strand of GenBank AccessionNo. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 11 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2B14,proximal end. The human homolog is the (−) strand of GenBank AccessionNo. NG_(—)001333.1, T-ell receptor beta.

SEQ ID NO: 12 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2B15,distal end. The human homolog is the (+) strand of GenBank Accession No.NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 13 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2B15,proximal end. The human homolog is the (−) strand of GenBank AccessionNo. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 14 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2B16,proximal end. The human homolog is the (−) strand of GenBank AccessionNo. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 15 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E23,distal end. The human homolog is the (−) strand of GenBank Accession No.NG_(—)001333.1, T-ell receptor beta.

SEQ ID NO: 16 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E23,proximal end. The human homolog is the (+) strand of GenBank AccessionNo. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 17 is a nucleic acid sequence associated with viral such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E24,proximal end. The human homolog is the (+) strand of GenBank AccessionNo. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 18 is a nucleic acid sequence associated with viral such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E25,proximal end. The human homolog is the (+) strand of GenBank AccessionNo. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 19 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E26,proximal end. The human homolog is the (+) strand of GenBank AccessionNo. NG_(—)001333.1, T-ell receptor beta.

SEQ ID NO: 20 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 18BD,proximal end. The human homolog is the (+) strand of GenBank AccessionNo. M16834.1, T-ell receptor V-D-J-beta 2.1 chain (described in WO02/057414 and Reynolds et al., Cell 50(1):107-17, 1987).

SEQ ID NO: 21 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 18E7,distal end. The human homolog is the (−) strand of GenBank Accession No.AC004593.1 including beta-chimerin rho GTPase (CHN2) (for example see WO01/12659).

SEQ ID NO: 22 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 18E7,proximal end. The human homologs are the (−) strand of GenBank AccessionNo. NG_(—)001333.1, T-cell receptor beta; and the (+) strand of GenBankAccession No. AC004593.1 including beta-chimaerin (CHN2).

SEQ ID NO: 23 is a nucleic acid sequence associated with viral, such asHIV and influenza A, infection, and is the clone identified asNucleotide Sequence 18E6, distal end. The human homolog is the (+)strand of GenBank Accession No. AL049699.8, including malic enzyme 1(ME1) NADP(+dependent cytosolic. Further information on this gene can befound in WO 01/55301 and WO 01/53312.

SEQ ID NO: 24 is a nucleic acid sequence associated with viral, such asHIV and influenza A, infection, and is the clone identified asNucleotide Sequence 18BD, distal end. The human homolog is the (+)strand of GenBank Accession No. AC123903.1, including hypotheticalprotein XP_(—)174419.

SEQ ID NO: 25 is a nucleic acid sequence associated with viral, such asHIV and influenza A, infection, and is the clone identified asNucleotide Sequence 18E9, distal end. The human homolog is the (+)strand of GenBank Accession No. AC096736.3, a region of chromosome4q31.3-32.

SEQ ID NO: 26 is a nucleic acid sequence associated with viral, such asHIV and influenza A, infection, and is the clone identified asNucleotide Sequence 18E9, middle of insert. The human homolog is the (+)strand of GenBank Accession No. AC096736.3, a region of chromosome4q31.3-32.

SEQ ID NO: 27 is a nucleic acid sequence associated with viral, such asHIV and influenza A, infection, and is the clone identified asNucleotide Sequence 18E9, proximal end. The human homologs are the (−)strand of GenBank Accession No. NG_(—)001333.1, T-cell receptor beta;and (−) strand of GenBank Accession No. AC096736.3, a region ofchromosome 4q31.3-32.

SEQ ID NO: 28 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E21,distal end. The human homolog is the (−) strand of GenBank Accession No.M26920.1, alpha satellite DNA.

SEQ ID NO: 29 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E22,distal end. The human homologs are the (+) strand of GenBank AccessionNo. AP004369.3, including LOC253788 (and neighboring similar to RIKENcDNA 1700001L23 (LOC219938)); and the (+) strand of GenBank AccessionNo. AC093117.2, between coagulation factor III, thromboplastin, tissuefactor (F3) and LOC91759.

SEQ ID NO: 30 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2B13,distal end. The human homolog is the (−) strand of GenBank Accession No.AC092043.2, between similar to zinc finger protein 7 KOX4 (LOC131880)and LOC166140.

SEQ ID NO: 31 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2B14, distal end. The human homologs are the (−) strand of GenBankAccession No. AL136963.17, between LOC222474 and similar to Rho guaninenucleotide exchange factor 4, isoform a, APC-stimulated guaninenucleotide exchange factor (LOC221178); and the (+) strand of GenBankAccession No. NG_(—)001333.1, T-ell receptor beta.

SEQ ID NO: 32 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2B16,distal end. The human homolog is the (−) strand of GenBank Accession No.AL133293.28, between ribosomal protein L7A-like 4 (RPL7AL4) and v-srcsarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) (SRC).

SEQ ID NO: 33 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E24,distal end. The human homolog is the (−) strand of GenBank Accession No.AL161417.17, KIAA0564.

SEQ ID NO: 34 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E25,distal end. The human homologs are the (−) strand of GenBank AccessionNo. Z12006.1, alpha satellite DNA; and the (+) and (−) strands ofGenBank Accession No. AC093577.2, M96 protein.

SEQ ID NO: 35 is a nucleic acid sequence associated with viral, such asHIV, infection, and is the clone identified as Nucleotide Sequence 2E26,distal end. The human homologs are the (−) strand of GenBank AccessionNo. Z78022.1, hypothetical protein similar to G proteins, especiallyRAP-2A (LOC57826); and the (+) strand of GenBank Accession No.AL136220.14, between LOC161005 and osteoblast specific factor 2(fasciclin I-like; OSF-2).

SEQ ID NO: 36 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B3B1, distal end. The canine homolog is the (+) and (−) strandportions of GenBank Accession No. AJ012166.1, Canis familiaris TCTAgene, AMT gene, DAG1 gene, and BSN gene.

SEQ ID NO: 37 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B5B5, distal end. The canine homolog is the (+) and (−) strandportions of GenBank Accession No. AJ012166.1, Canis familiaris TCTAgene, AMT gene, DAG1 gene, and BSN gene.

SEQ ID NO: 38 is a nucleic acid sequence associated with vial, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1B1, distal end The human homolog is the (+) strand of GenBankAccession No. AC117507.5, including LIM domain containing preferredtranslocation partner in lipoma (LPP).

SEQ ID NO: 39 is a nucleic acid sequence associated with viral such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1B2, distal end. The human homolog is the (−) strand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 40 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1B4, distal end. The human homolog is the (−) strand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 41 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1B5, distal end. The human homolog is the (−) strand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 42 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1B6, distal end. The human homolog is the (−) strand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 43 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1E3, entire insert. The human homolog is the (+) strand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 44 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1E5, proximal end. The human homolog is the (−) strand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 45 is a nucleic acid sequence associated with viral such asinfluenza A, infection, and is the clone identified as NucleotideSequence B6B1, entire insert. The human homolog is the (−) strand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 46 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B6E1, distal end. The human homolog is the (+) strand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 47 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B6E1, proximal end. The human homolog is the (−) stand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 48 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B6E3, proximal end. The human homolog is the (−) stand ofGenBank Accession No. AC117507.5, including LIM domain containingpreferred translocation partner in lipoma (LPP).

SEQ ID NO: 49 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1E1, distal end. The human homolog is the (+) strand ofGenBank Accession No. AC104036.8, between LOC253121 and hyaluronansynthase 2 (HAS2).

SEQ ID NO: 50 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1E1, proximal end. The human homolog is the (−) strand ofGenBank Accession No. AF260225.1, Testin 2 and Testin 3 (see WO01/57270, WO 01/57271, WO 01/57273, WO 01/57274, WO 01/57275, WO01/57276, WO 01/57277, WO 01/57278, or Tatarelli et al., Genomics68(1):1-12, 2000).

SEQ ID NO: 51 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1E4, distal end. The human homolog is the (+) strand ofGenBank Accession No. AF260225.1, Testin 2 and Testin 3.

SEQ ID NO: 52 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B1E4, proximal end. The human homolog is the (−) strand ofGenBank Accession No. AF260225.1, Testin 2 and Testin 3.

SEQ ID NO: 53 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B6E2, distal end. The human homolog is the (+) strand ofGenBank Accession No. AF260225.1, Testin 2 and Testin 3.

SEQ ID NO: 54 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B6E2, proximal end. The human homolog is the (−) strand ofGenBank Accession No. AF260225.1, Testin 2 and Testin 3.

SEQ ID NO: 55 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B6E4, proximal end. The human homolog is the (−) strand ofGenBank Accession No. AF260225.1, Testin 2 and Testin 3.

SEQ ID NO: 56 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B7E1, distal end. The human homolog is the (+) strand ofGenBank Accession No. AF260225.1, Testin 2 and Testin 3.

SEQ ID NO: 57 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B7E1, proximal end. The human homolog is the (−) strand ofGenBank Accession No. AF260225.1, Testin 2 and Testin 3.

SEQ ID NO: 58 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B5E2, distal end. The human homolog is the (−) strand ofGenBank Accession No. AL133230.25, PTPN1 gene for protein tyrosinephosphatase, non-receptor type 1 (see Watanabe et al., Jpn. J. CancerRes. 93:1114-22, 2002).

SEQ ID NO: 59 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B5E2, middle of insert. The human homolog is the (−) strand ofGenBank Accession No. AL133230.25, PTPN1 gene for protein tyrosinephosphatase, non-receptor type 1.

SEQ ID NO: 60 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B3E11, distal end. The human homolog is the (+) strand ofGenBank Accession No. AL445675.9, between LOC149360 and LOC253961.

SEQ ID NO: 61 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B3E11, proximal end. The human homolog is the (−) strand ofGenBank Accession No. AL391986.12, between KIKAA1560 and Tectorin beta(TECTB).

SEQ ID NO: 62 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B6E3, distal end. The human homolog is the (−) strand ofGenBank Accession No. AC016826.9, including Cadherin related 23 (CDH23).

SEQ ID NO: 63 is a nucleic acid sequence associated with viral, such asinfluenza A, infection, and is the clone identified as NucleotideSequence B6B4, distal end. The human homolog is the (+) strand ofGenBank Accession No. AL357372.12, Myeloid/lymphoma or mixed lineageleukemia, translocated to 10 (MNMLT10).

SEQ ID NO: 64 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceZV1-1B5, distal end. The human homolog is the (−) strand of GenBankAccession No. AL355802.13, between exportin 5 (XPO5) and DNA polymeraseeta (POLH).

SEQ ID NO: 65 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceZV1-1B5, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL355802.13, between XPO5 and POLH.

SEQ ID NO: 66 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceZV1-1E, proximal end. The human homolog is the (−) stand of GenBankAccession No. AL355802.13, between XPO5 and POLH.

SEQ ID NO: 67 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2E1, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL135744.4, including heterogenous nuclear riboprotein C(C1/C2) (HNRPC).

SEQ ID NO: 68 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2E5, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL135744.4, including HNRPC.

SEQ ID NO: 69 is a nucleic acid sequence associated with viral such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2E6, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL135744.4, including HNRPC.

SEQ ID NO: 70 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2B2, proximal end. The human homolog is the (−) strand of GenBankAccession No. ALI35744.4, including HNRPC.

SEQ ID NO: 71 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2B13, proximal end. The human homolog is the (−) strand of GenBankAccession No. ALI35744.4, including HNRPC.

SEQ ID NO: 72 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2B14, proximal end. The human homolog is the (−) strand of GenBankAccession No. AL135744.4, including HNRPC.

SEQ ID NO: 73 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2B21, proximal end. The human homolog is the (−) strand of GenBankAccession No. AL135744.4, including HNRPC.

SEQ ID NO: 74 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2B25, proximal end. The human homolog is the (−) strand of GenBankAccession No. AL135744.4, including HNRPC.

SEQ ID NO: 75 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2B35, proximal end. The human homolog is the (−) strand of GenBankAccession No. ALI 35744.4, including HNRPC.

SEQ ID NO: 76 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2E5, distal end. The human homolog is the (+) and (−) strands ofGenBank Accession No. AL050324.5, including alpha-endosulfine pseudogene(ENSAP) and LOC128741.

SEQ ID NO: 77 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2E6, distal end. The human homolog is the (+) strand of GenBankAccession No. AC017060.7, including LOC222888.

SEQ ID NO: 78 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2B13, distal end. The human homolog is the (+) strand of GenBankAccession No. AL161731.20, between LOC138421 and zinc finger protein297B (ZNF297B).

SEQ ID NO: 79 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2B14, distal end. The human homolog is the (−) strand of GenBankAccession No. AC012366.10, including sideroflexin 5 (SFXN5).

SEQ ID NO: 80 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV1-2B35, distal end. The human homolog is the (+) strand of GenBankAccession No. AL645504.10, including importin 9 (FLJ10402).

SEQ ID NO: 81 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceGV1-1B1, distal end. The human homolog is the (+) strand of GenBankAccession No. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 82 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceGV1-1B1, proximal end. The human homolog is the (+) strand of GenBankAccession No. NG_(—)001333.1, T-cell receptor beta.

SEQ ID NO: 83 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-B1, distal end. The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 84 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E2, distal end. The human homolog is the (+) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 85 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E2, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 86 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E3, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 87 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E4, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 88 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E5, distal end. The human homolog is the (+) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 89 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E5, proximal en The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 90 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-B1, distal ends The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 91 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E2, distal end. The human homolog is the (+) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 92 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E2, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 93 is a nucleic acid sequence associated with viral such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E4, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 94 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-B1, distal end. The human homolog is the (+) and (−) strand ofGenBank Accession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 95 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E1, distal end The human homolog is the (+) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 96 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E1, proximal end. The human homolog is the (−) stand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 97 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E4, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 98 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E5, distal end. The human homolog is the (+) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 99 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E5, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC058791.4, adjacent to LOC135952.

SEQ ID NO: 100 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E1, distal end. The human homolog is the (+) stand of GenBankAccession No. AC021753.7, hypothetical protein KIAA1259.

SEQ ID NO: 101 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E1, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC021753.7, hypothetical protein KIAA1259.

SEQ ID NO: 102 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E3, distal end. The human homolog is the (+) and (−) strands ofGenBank Accession No. AC107081.5, copper metabolism gene (MURR1) andchaperonin containing TCP1, subunit 4 (CCT4).

SEQ ID NO: 103 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E4, distal end. The human homolog is the (−) strand of GenBankAccession No. AC099785.2, hypothetical protein FLJ40773 and similar toribosomal protein L24-like (LOC149360).

SEQ ID NO: 104 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E4, distal end. The human homolog is the (+) strand of GenBankAccession No. AF260225.1, Testin 2 and 3 (TES).

SEQ ID NO: 105 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV2-E4, proximal end. The human homolog is the (−) strand of GenBankAccession No. AF260225.1, Testin 2 and 3 (TES).

SEQ ID NO: 106 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E7, distal end. The human homolog is the (+) strand of GenBankAccession No. AF260225.1, Testin 2 and 3 (TES).

SEQ ID NO: 107 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E7, proximal end. The human homolog is the (−) strand of GenBankAccession No. AF260225.1, Testin 2 and 3 (TES).

SEQ ID NO: 108 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-B2, distal end. The human homolog is the (+) and (−) strands ofGenBank Accession No. AC105934.2, polybromo 1 (PB1).

SEQ ID NO: 109 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-B4, distal end. The human homolog is the (+) strand of GenBankAccession No. AC022506.38, between DNA damage inducible transcript 3(DDIT3) and KIAA1887.

SEQ ID NO: 110 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-B5, distal end. The human homolog is the (−) strand of GenBankAccession No. AL157834.12, PDZ and LIM domain 1 (elfin) (PDLIM1).

SEQ ID NO: 111 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E1, distal end. The human homolog is the (+) strand of GenBankAccession No. AL110115.38, LOC284803.

SEQ ID NO: 112 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E1, proximal end. The human homolog is the (−) strand of GenBankAccession No. AL110115.38, signal peptide peptidase (HM13) andLOC284803.

SEQ ID NO: 113 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E3, distal end. The human homolog is the (−) strand of GenBankAccession No. AL117341.26, containing PRO0097 and adjacent to FL31958.

SEQ ID NO: 114 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E3, proximal end. The human homolog is the (−) strand of GenBankAccession No. AP002076.3, small inducible cytokine E, member 1(endothelial monocyte-activating) (SCYE1).

SEQ ID NO: 115 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E6, distal end. The human homolog is the (+) strand of GenBankAccession No. AP002076.3, containing SCYE1.

SEQ ID NO: 116 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E6, proximal end. The human homolog is the (−) strand of GenBankAccession No. AP002076.3, containing SCYE1.

SEQ ID NO: 117 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E4, distal end. The human homolog is the (+) and (−) strands ofGenBank Accession No. AC132812.9, between E3 ubiquitin ligase (SMURF2)and hypothetical protein MGC40489.

SEQ ID NO: 118 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E5, distal end. The human homolog is the (+) strand of GenBankAccession No. AC079383.17, Ras oncogene family member Rab9.

SEQ ID NO: 119 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV3-E5, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC079383.17, Ras oncogene family member Rab9.

SEQ ID NO: 120 is a nucleic acid sequence associated with viral such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E2, distal end. The human homolog is the (−) strand of GenBankAccession No. AL132989.5, between PRO1617 and retinoblastoma bindingprotein 1 (RBBP1).

SEQ ID NO: 121 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E2, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL132989.5, RBBP1.

SEQ ID NO: 122 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E3, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL132989.5, retinoblastoma binding protein 1 (RBBP1).

SEQ ID NO: 123 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E3, distal end. The human homolog is the (+) and (−) strands ofGenBank Accession No. AC096669.1, a region of chromosome 2q12.

SEQ ID NO: 124 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV6-E4, distal end. The human homolog is the (−) strands of GenBankAccession No. AF196968.4, elongation factor for selenoproteintranslation (SELB).

SEQ ID NO: 125 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-B1, distal end. The human homolog is the (−) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 126 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-B1, proximal end. The human homolog is the (+) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 127 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E1, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 128 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E1, distal end. The human homolog is the (+) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 129 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E2, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 130 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E3, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 131 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E4, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC1112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 132 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E5, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 133 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E6, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 134 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E7, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 135 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E8, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 136 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E9, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC112218.2, transcription factor SMIF (HSA275986).

SEQ ID NO: 137 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E10, proximal end. The human homolog is the (−) strand of GenBankAccession Neo. AC112218.2, transcription factor SMIF (HSA75986).

SEQ ID NO: 138 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E2, distal end. The human homolog is the (+) strand of GenBankAccession No. AL031293.1, KIAA1026.

SEQ ID NO: 139 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E3, distal end. The human homolog is the (+) strand of GenBankAccession No. AL035587.5, trinucleotide repeat containing 5 (TNRC5).

SEQ ID NO: 140 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E4, distal end. The human homolog is the (−) strand of GenBankAccession No. AC126182.2, homogentisate 1,2-dioxygenase (HGD).

SEQ ID NO: 141 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E5, distal end. The human homolog is the (+) strand of GenBankAccession No. AL591643.4, a region of chromosome Xq23-24.

SEQ ID NO: 142 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E6, distal end. The human homolog is the (−) strand of GenBankAccession No. AC113603.3, a region of chromosome 4p15.3.

SEQ ID NO: 143 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E7, distal end. The human homolog is the (+) strand of GenBankAccession No. AC011995.8, similar to LWamide neuropeptide precursorprotein [Hydractinia echinata] (LOC129883).

SEQ ID NO: 144 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E8, distal end. The human homolog is the (−) stand of GenBankAccession No. AC084208.5, a region of chromosome 2q21.

SEQ ID NO: 145 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E9, distal end. The human homolog is the (−) strand of GenBankAccession No. AL391259.15, a region of chromosome Xp11.4, includingubiquitin specific protease 9 (USP9X).

SEQ ID NO: 146 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV13-E10, distal end. The human homolog is the (+) strand of GenBankAccession No. AC006397.1, LOC221829.

SEQ ID NO: 147 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-B2, distal end. The human homolog is the (+) strand of GenBankAccession No. X14945.1, U3 small nuclear RNA gene.

SEQ ID NO: 148 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-B2, proximal end. The human homolog is the (+) stand of GenBankAccession No. X14945.1, U3 small nuclear RNA gene.

SEQ ID NO: 149 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-E1, proximal end. The human homolog is the (−) strand of GenBankAccession No. X14945.1, U3 small nuclear RNA gene.

SEQ ID NO: 150 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-E2, proximal end. The human homolog is the (−) strand of GenBankAccession No. X14945.1, U3 small nuclear RNA gene.

SEQ ID NO: 151 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-E2, distal end. The human homolog is the (−) stand of GenBankAccession No. X14945.1, U3 small nuclear RNA gene.

SEQ ID NO: 152 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-E5, proximal end. The human homolog is the (−) strand of GenBankAccession No. X14945.1, U3 small nuclear RNA gene.

SEQ ID NO: 153 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV8-E1, proximal end. The human homolog is the (−) strand of GenBankAccession No. X14945.1, U3 small nuclear RNA gene.

SEQ ID NO: 154 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV8-E1, distal end. The human homolog is the (+) strand of GenBankAccession No. X14945.1, U3 small nuclear RNA gene.

SEQ ID NO: 155 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-B3, distal end. The human homolog is the (+) strand of GenBankAccession No. AL365203.19, integrin, beta 1 (UrGB1).

SEQ ID NO: 156 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-B3, proximal end. The human homolog is the (−) strand of GenBankAccession No. AL365203.19, ITGB1.

SEQ ID NO: 157 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-E3, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL365203.19, ITGB1.

SEQ ID NO: 158 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-E3, distal end. The human homolog is the (−) strand of GenanBAccession No. AL365203.19, ITGB1.

SEQ ID NO: 159 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-E1, distal end. The human homolog is the (+) strand of GenBankAccession No. AP001132.4, acrosomal vesicle protein 1 (ACRV1) and CHK1checkpoint homolog (CHEK1).

SEQ ID NO: 160 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV7-E5, distal end. The human homolog is the (−) strand of GenBankAccession No. AK025453.1, prospero-related homeobox 1 (PROX1).

SEQ ID NO: 161 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E1, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 162 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E2, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 163 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E3, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 164 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E4, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 165 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E4, distal end. The human homolog is the (−) strand of GenBankAccession No. AL590543.8, between hypothetical proteins FLJ20627 andFLJ12910.

SEQ ID NO: 166 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E5, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 167 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E8, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 168 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E9, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 169 is a nucleic acid sequence associated with viral such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E9, distal end. The human homolog is the (−) strand of GenBankAccession No. AL590543.8, between hypothetical proteins FLJ20627 andFLJ12910.

SEQ ID NO: 170 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E10, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 171 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E10, distal end. The human homolog is the (−) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 172 is a nucleic acid sequence associated with viral such asEbola, infection, and is the clone identified as Nucleotide SequenceMV19-E2, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ20627.

SEQ ID NO: 173 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV19-E2, distal end. The human homolog is the (−) strand of GenBankAccession No. AL590543.8, between hypothetical proteins FLJ20627 andFLJ12910.

SEQ ID NO: 174 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E1, distal end. The human homolog is the (+) strand of GenBankAccession No. AC105001.3, between PIN2-interacting protein 1 (PINX1) andSRY (sex-determining region Y)-box7 (SOX7).

SEQ ID NO: 175 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E2, distal end. The human homolog is the (−) strand of GenBankAccession No. AC009520.16, LOC131920.

SEQ ID NO: 176 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E3, distal end. The human homolog is the (−) strand of GenBankAccession No. AL596329.5, a region of chromosome 13q14.

SEQ ID NO: 177 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E5, distal end. The human homolog is the (+) strand of GenBankAccession No. AC023844.6, neurotrophic tyrosine kinase, receptor, type 3(NTRK3).

SEQ ID NO: 178 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E7, promimal end. The human homolog is the (−) strand of GenBankAccession No. AC024940.39, between TERA protein (TERA) and hypotheticalprotein FLJ13224.

SEQ ID NO: 179 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E7, distal end. The human homolog is the (+) strand of GenBankAccession No. AC024940.39, flanking TERA protein (TERA) and hypotheticalprotein FLJ13224.

SEQ ID NO: 180 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E8, distal end. The human homolog is the (−) stand of GenBankAccession No. AC084335.6, hypothetical gene LOC284260.

SEQ ID NO: 181 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E11, proximal end. The human homolog is the (+) strand of GenBankAccession No. AC073108.9, POM (POM121 homolog) and ZP3 fusion (POMZP3).

SEQ ID NO: 182 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV14-E11, distal end. The human homolog is the (−) strand of GenBankAccession No. AC073108.9, POM (POM121 homolog) and ZP3 fusion (POMZP3).

SEQ ID NO: 183 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV19-E4, distal end. The human homolog is the (+) strand of GenBankAccession No. AC087650.12, between DEAD/H box polypeptide 8 (DDX8) andsimilar to ribosomal protein L29 (cell surface heparin binding proteinHIP) (LOC284064).

SEQ ID NO: 184 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV20-E2, distal end. The human homolog is the (−) stand of GenBankAccession No. AC105285.3, LOC345307 andUDP-N-acetyl-D-galactosamine:polypeptideN-acetylgalactosaminyltransferase 7 (GALNT7).

SEQ ID NO: 185 is a nucleic acid sequence associated with viral such asEbola, infection, and is the clone identified as Nucleotide SequenceMV20-E2, proximal end. The human homolog is the (+) strand of GenBankAccession No. AC105285.3, LOC345307 andUDP-N-acetyl-D-galactosmine:polypeptideN-acetylgalactosaminyltransferase 7 (GALNT7).

SEQ ID NO: 186 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV20-B1, distal end. The human homolog is the (+) strand of GenBankAccession No. AC105285.3, LOC345307 andUDP-N-acetyl-D-galactosamine:polypeptideN-acetylgalactosaminyltransferase 7 (GALNT7).

SEQ ID NO: 187 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV20-E3, distal end. The murine homolog is the (+) strand of GenBankAccession No. NG_(—)001440.1, Mus musculus 55 rRNA pseudogene(Rn5_(s)-ps1).

SEQ ID NO: 188 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV20-E5, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL121886.22, between ribosomal protein L27a pseudogene(RPL27AP) and v-myb myeloblastosis viral oncogene homolog-like 2(MYBL2).

SEQ ID NO: 189 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E2, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL121886.22, between RPL27AP and MYBL2.

SEQ ID NO: 190 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E6, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL121886.22, between RPL27AP and MYBL2.

SEQ ID NO: 191 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E9, proximal end. The human homolog is the (+) stand of GenBankAccession No. AL121886.22, between RPL27AP and MYBL2.

SEQ ID NO: 192 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E9, distal end. The human homolog is the (−) strand of GenBankAccession No. AL121886.22, between RPL27AP and MYBL2.

SEQ ID NO: 193 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV20-E6, distal end. The human homolog is the (+) strand of GenBankAccession No. AP000711.4, Down's syndrome cell adhesion molecule like 1(DSCAML1).

SEQ ID NO: 194 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV20-E7, distal end. The human homolog is the (+) strand of GenBankAccession No. AL391555.19, LOC148529.

SEQ ID NO: 195 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV20-B4, distal end. The human homolog is the (−) strand of GenBankAccession No. AC112129.4, Huntingtin-associated protein interactingprotein (HAPIP).

SEQ ID NO: 196 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E1, proximal end. The human homolog is the (−) stand of GenBankAccession No. Z69732.1, between LOC158525 and similar to RIKEN cDNA1210001E11 (LOC347366).

SEQ ID NO: 197 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E3, proximal end. The human homolog is the (−) strand of GenBankAccession No. Z69732.1, between LOC158525 and similar to RIKEN cDNA1210001E11 (LOC347366).

SEQ ID NO: 198 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E5, proximal end. The human homolog is the (−) strand of GenBankAccession No. Z69732.1, between LOC158525 and similar to RIKEN cDNA1210001E11 (LOC347366).

SEQ ID NO: 199 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E5, proximal end. The human homolog is the (−) strand of GenBankAccession No. Z69732.1, between LOC158525 and similar to RIKEN cDNA1210001E11 (LOC347366).

SEQ ID NO: 200 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E8, proximal end. The human homolog is the (−) strand of GenBankAccession No. Z69732.1, between LOC158525 and similar to RIKEN cDNA1210001E11 (LOC347366).

SEQ ID NO: 201 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E2, distal end. The human homolog is the (−) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ12910.

SEQ ID NO: 202 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E2, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ12910.

SEQ ID NO: 203 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E6, distal end. The human homolog is the (−) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ12910.

SEQ ID NO: 204 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E6, proximal end. The human homolog is the (+) strand of GenBankAccession No. AL590543.8, hypothetical protein FLJ12910.

SEQ ID NO: 205 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E7, distal end. The human homolog is the (+) strand of GenBankAccession No. AC005284.1, LOC350411.

SEQ ID NO: 206 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV22-E9, proximal end. The human homolog is the (+) strand of GenBankAccession No. AP000505.1, between allograft inflammatory factor 1 (AIF1)and HLA-B associated transcript 2 (BAT2).

SEQ ID NO: 207 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV27-E1, distal end. The human homolog is the (−) strand of GenBankAccession No. AC008755.8, C19orf7.

SEQ ID NO: 208 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV27-E2, distal end. The human homolog is the (+) strand of GenBankAccession No. AC058791.4, between LOC346658 and LOC340349.

SEQ ID NO: 209 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV27-E2, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC058791.4, between LOC346658 and LOC340349.

SEQ ID NO: 210 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV27-E3, distal end. The human homolog is the (+) strand of GenBankAccession No. AC079030.13, a region of chromosome 12q21.

SEQ ID NO: 211 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV27-E3, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC139138.2, between LOC339248 and hypothetical proteinFLJ22659.

SEQ ID NO: 212 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV27-E4, distal end. The human homolog is the (−) strand of GenBankAccession No. AL513550.9, between SR rich protein DKFZp564B0769 andhypothetical protein MGC14793.

SEQ ID NO: 213 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-B1, distal end. The human homolog is the (−) stand of GenBankAccession No. AP001160.4, hypothetical protein FLJ10439.

SEQ ID NO: 214 is a nucleic acid sequence associated with vial, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-B1, proximal end. The human homolog is the (+) strand of GenBankAccession No. AP001160.4, hypothetical protein FLJ10439.

SEQ ID NO: 215 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-B3, distal end. The human homolog is the (+) strand of GenBankAccession No. AC090826.15, between cytochrome P450, family 11, subfamilyA, polypeptide 1 (CYP11A1) and sema domain, immunoglobulin domain (Ig)and GPI membrane anchor, (semaphoring) 7A.

SEQ ID NO: 216 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-B3, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC090826.15, between cytochrome P450, family 11, subfamilyA, polypeptide 1 (CYP11A1) and sema domain, immunoglobulin domain (Ig)and GPI membrane anchor, (semaphoring) 7A.

SEQ ID NO: 217 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E11, proximal end. The human homolog is the (+) strand of GenBankAccession No. AC090826.15, between cytochrome P450, family 11, subfamilyA, polypeptide 1 (CYP11A1) and sema domain, immunoglobulin domain (Ig)and GPI membrane anchor, (semaphoring) 7A.

SEQ ID NO: 218 is a nucleic acid sequence associated with vial, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-EB11, distal end. The human homolog is the (−) strand of GenBankAccession No. AC090826.15, between cytochrome P450, family 11, subfamilyA, polypeptide 1 (CYP11A1) and sema domain, immunoglobulin domain (Ig)and GPI membrane anchor, (semaphoring) 7A.

SEQ ID NO: 219 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E1, proximal end. The human homolog is the (−) strand of GenBankAccession No. AC011500.7, ribosomal protein S16 (RPS16).

SEQ ID NO: 220 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E1, distal end. The human homolog is the (+) stand of GenBankAccession No. AC011500.7, ribosomal protein S16 (RPS16).

SEQ ID NO: 221 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E4, distal end. The human homolog is the (−) strand of GenBankAccession No. AC091172.11, between hypothetical protein DKFZp434H0115and ATP citrate lyase (ACLY).

SEQ ID NO; 222 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E4, proximal end. The human homolog is the (+) strand of GenBankAccession No. AC091172.11, between hypothetical protein DKFZp434H0115and ACLY.

SEQ ID NO: 223 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E7, distal end. The human homolog is the (+) strand of GenBankAccession No. AL035594.7, protein tyrosine phosphatase, receptor type, K(PTPRK).

SEQ ID NO: 224 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E7, proximal end. The human homolog is the (+) strand of GenBankAccession No. AC124857.2, calnexin (CANX) and (−) strand of GenBankAccession No. AL035594.7, protein tyrosine phosphatase, receptor type, K(PTPRK).

SEQ ID NO: 225 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E8, distal end. The human homolog is the (+) strand of GenBankAccession No. AC009144.5, cyclin M2 (CNNM2).

SEQ ID NO: 226 is a nucleic acid sequence associated with viral, such asEbola, infection, and is the clone identified as Nucleotide SequenceMV28-E8, proximal end. The human homolog is the (+) strand of GenBankAccession No. AC011510.7, AXL receptor tyrosine kinase (AXL).

SEQ ID NO: 227 is a nucleic acid sequence showing GenBank Accession No.BC008947, Homo sapiens chromosome 10 open reading frame 3, mRNA (cDNAclone MGC:3422 IMAGE:3028566). This sequence is associated with viralinfection, such as Ebola infection.

SEQ ID NO: 228 is an amino acid sequence encoded by SEQ ID NO: 227.

SEQ ID NO: 229 is a nucleic acid sequence showing GenBank Accession No.NM_(—)018131, Homo sapiens chromosome 10 open reading frame 3 (C10orf3).This sequence is associated with viral infection, such as Ebolainfection.

SEQ ID NO: 230 is an amino acid sequence encoded by SEQ ED NO: 229.

SEQ ID NO: 231 is a nucleic acid sequence showing GenBank Accession No.NM_(—)013451, Homo sapiens fer-1-like 3, myoferlin (C. elegans)(FER1L3), transcript variant 1, mRNA. This sequence is associated withviral infection, such as Ebola infection.

SEQ ID NO: 232 is an amino acid sequence encoded by SEQ ID NO: 231.

SEQ ID NOS: 233 and 234 are exemplary complementary primers.

SEQ ID NOS: 235-237 are primer sequences used to sequence the shuttleclones as described in Example 2.

SEQ ID NOS: 238-241 are Rab9 siRNA sequences.

SEQ ID NOS: 242-245 are AXL receptor tyrosine kinase siRNA sequences.

SEQ ID NOS: 246-295 are beta-chimerin receptor tyrosine kinase RNAisequences.

SEQ ID NOS: 296-345 are retinoblastoma binding protein 1 RNAi sequences.

SEQ ID NOS: 346-395 are Homo sapiens chromosome 10 open reading frame 3RNAi sequences.

SEQ ID NOS: 396-445 are Homo sapiens fer-1-like 3, myoferlin (C.elegans), transcript variant 1 RNAi sequences.

SEQ ID NOS: 446-495 are Homo sapiens chromosome 10 open reading frame 3(C10orf3) RNAi sequences.

SEQ ID NOS: 496-545 are malic enzyme RNAi sequences.

SEQ ID NOS: 546-595 are cadherin related 23 RNAi sequences.

SEQ ID NOS: 596-645 are sideroflexin 5 RNAi sequences.

SEQ ID NOS: 646-695 are polybromo 1 (PB1) RNAi sequences.

SEQ ID NOS: 696-720 are elongation factor for selenoprotein translationRNAi sequences.

SEQ ID NOS: 721-745 are integrin, beta 1 RNAi sequences.

SEQ ID NOS: 746-795 are huntingtin interacting protein 1 RNAi sequences.

SEQ ID NOS: 796-845 are cyclin M2 RNAi sequences.

DETAILED DESCRIPTION OF SEVERAL EMBODIMENTS Abbreviations and Terms

The following explanations of terms and methods are provided to betterdescribe the present disclosure and to guide those of ordinary skill inthe art in the practice of the present disclosure. The singular forms“a,” “an,” and “the” refer to one or more than one, unless the contextclearly dictates otherwise. For example, the term “comprising a nucleicacid” includes single or plural nucleic acids and is consideredequivalent to the phrase “comprising at least one nucleic acid.” Theterm “or” refers to a single element of stated alternative elements or acombination of two or more elements, unless the context clearlyindicates otherwise. For example, the phrase “a first nucleic acid or asecond nucleic acid” refers to the first nucleic acid, the secondnucleic acid, or a combination of both the first and second nucleicacids. As used herein, “comprises” means “includes.” Thus, “comprising apromoter and an open reading frame,” means “including a promoter and anopen reading frame,” without excluding additional elements.

Unless explained otherwise, all technical and scientific terms usedherein have the same meaning as commonly understood to one of ordinaryskill in the art to which this disclosure belongs. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present disclosure, suitable methods andmaterials are described below. The materials, methods, and examples areillustrative only and not intended to be limiting.

A=adenine

C=cytosine

DNA=deoxyribonucleic acid

ds=double-stranded (for example, dsDNA)

G=guanine

mg=milligram

ng=nanogram

PCR=polymerase chain reaction

Pu=purine

Py=pyrimidine

RNA=ribonucleic acid

mRNA=messenger RNA

MOI=multiplicity of infection

siRNA=short interfering or interrupting RNA

ss=single-stranded (for example, ssDNA)

T=thymine

T_(m)=melting temperature

U=uracil

μg=microgram

μl=microliter

Amplification of a nucleic acid. To increase the number of copies of anucleic acid. Several methods can be used to amplify a nucleic acid,such as polymerase chain reaction (PCR). Other examples of amplificationinclude, but are not limited to, strand displacement amplification (U.S.Pat. No. 5,744,311); transcription-free isothermal amplification (U.S.Pat. No. 6,033,881); repair chain reaction amplification (WO 90/01069);ligase chain reaction amplification (European Patent Appl. 320 308); gapfilling ligase chain reaction amplification (U.S. Pat. No. 5,427,930);and NASBA™ RNA transcription-free amplification (U.S. Pat. No.6,025,134).

The amplification products (“amplicons”) can be further processed,manipulated, or characterized by electrophoresis, restrictionendonuclease digestion, hybridization, nucleic acid sequencing,ligation, or other molecular biology techniques. Standard protocols canbe modified. For example, PCR can be modified by using reversetranscriptase PCR (RT-PCR) to amplify RNA molecules.

Antisense, Sense, and Antigene. Antisense molecules are molecules thatare specifically hybridizable or specifically complementary to eitherRNA or the plus strand of DNA. Sense molecules are molecules that arespecifically hybridizable or specifically complementary to the minusstrand of DNA. Antigene molecules are either antisense or sensemolecules directed to a particular dsDNA target. These molecule can beused to interfere with gene expression.

Double-stranded DNA (dsDNA) has two strands, a 5′ to 3′ strand, referredto as the plus (+) strand, and a 3′ to 5′ strand (the reversecomplement), referred to as the minus (−) strand. Because RNA polymeraseadds nucleic acids in a 5′ to 3′ direction, the minus strand of the DNAserves as the template for the RNA during transcription. Thus, the RNAformed will have a sequence complementary to the minus strand andvirtually identical to the plus strand, except that U is substituted forT in RNA molecules.

Array. An arrangement of biological samples or molecules, such as anarrangement of tissues, cells, or biological macromolecules (including,but not limited to, peptides or nucleic acids) in addressable locationson or in a substrate. The arrangement of molecules within the array canbe regular, such as being arranged in uniform rows and columns, orirregular. The number of addressable locations within the array canvary, for example from a few (such as two or three) to more than 50,100, 200, 500, 1000, 10,000, or more. In certain examples, the arrayincludes one or more molecules or samples occurring on the array aplurality of times (twice or more) to provide an added feature to thearray, such as redundant activity or to provide internal controls. A“microarray” is an array that is miniaturized and evaluated or analyzedusing microscopy.

Within an array, each arrayed sample or molecule is addressable, suchthat its location can be reliably and consistently determined within theat least two dimensions of the array. The location or address of eachsample or molecule can be assigned when it is applied to the array, anda key or guide can be provided in order to correlate each location withthe appropriate target sample or molecule position. Ordered arrays canbe arranged in a symmetrical grid pattern or other patterns, forexample, in radially distributed lines, spiral lines, or orderedclusters. Addressable arrays can be computer readable; a computer can beprogrammed to correlate a particular address on the array withinformation about the sample at that position, such as hybridization orbinding data, including signal intensity. In some exemplary computerreadable formats, the individual samples or molecules in the array arearranged regularly (for example, in a Cartesian grid pattern), which canbe correlated to address information by a computer.

The sample or molecule addresses on an array can assume many differentshapes. For example, substantially square regions can be used asaddresses within arrays, but addresses can be differently shaped, forexample, substantially rectangular, triangular, oval, irregular, oranother shape. The term “spot” refers generally to a localized placementof molecules, tissue or cells, and is not limited to a round orsubstantially round region or address.

Examples of macroarrays include the Histo™-array and INSTA-blot™ linesof products available from Imgenix, Inc. (San Diego, Calif.) and the MaxArray™ line of products available from Zymed Laboratories, Inc. (SouthSan Francisco, Calif.), while exemplary microarrays include the variousGeneChip® technologies and products available from Affymetrix, Inc.(Santa Clara, Calif.) and the Hilight™, Label Star™, and Array-ReadyOligo Set lines of products available from Qiagen, Inc. (Valencia,Calif.).

β-chimerin. The term β-chimerin includes any β-chimerin gene, cDNA, RNA,or protein from any organism and is a β-chimerin that can function as atype of rho-GTPase. In some examples, β-chimerin is involved in viralinfection.

Rho-GTPases are a family of small GTPases implicated as components ofcellular signal transduction cascades. Signals that pass throughrho-GTPase cascades can be initiated by the activation of cell surfaceproteins, such as growth factors. Functions of signaling cascadesmediated by rho-GTPases, include, but are not limited to, alterations incellular morphology which are linked to processes such as immune cellfunction, oncogenesis, metastasis and certain diseases (Peck, FEBS Lett.528:27, 2002).

Examples of native β-chimerin nucleic acid sequences include, but arenot limited to those shown in SEQ ID NOS: 21-22 (such as a targetsequence associated with SEQ ID NOS: 21-22), as well as the proteinsequence encoded thereby. This cell line remains CD4⁺ after exposure toHIV 1 and HIV 2 and is resistant to HIV infection. β-chimerin alsoincludes variants, fusions, and fragments of the disclosed nucleic acidand amino acid sequences that retain β-chimerin biological activity.

Examples of β-chimerin amino acid sequences include, but are not limitedto: Genbank Accession Nos: NM_(—)004067 (mRNA) and NP_(—)004058.1(protein). In one example, a β-chimerin sequence includes a full-lengthwild-type (or native) sequence, as well as β-chimerin allelic variants,variants, fragments, homologs or fusion sequences that retain theability to function as a type of rho-GTPase. In certain examples,β-chimerin has at least 80% sequence identity, for example at least 85%,90%, 95%, or 98% sequence identity to a native β-chimerin.

cDNA (complementary DNA). A piece of DNA lacking internal, non-codingsegments (introns) and transcriptional regulatory sequences. A cDNA alsocan contain untranslated regions (UTRs) that are responsible fortranslational control in the corresponding RNA molecule. cDNA can beproduced using various methods, such as synthesis in the laboratory byreverse transcription from messenger RNA extracted from cells.

Complementary. Complementary binding occurs when the base of one nucleicacid molecule forms a hydrogen bond the base of another nucleic acidmolecule. Normally, the base adenine (A) is complementary to thymidine(T) and uracil (U), while cytosine (C) is complementary to guanine (G).For example, the sequence 5′-ATCG-3′ of one ssDNA molecule can bond to3′-TAGC-5′ of another ssDNA to form a dsDNA.

Nucleic acid molecules can be complementary to each other even withoutcomplete hydrogen-bonding of all bases of each molecule. By way ofexample only (and without limitation), the ssDNA: 5′-GCTTGCCAAACCTACA-3′(SEQ ID NO: 233) is considered complementary to the ssDNA3′-CGAACGGTCTGGATOT-5′ (SEQ ID NO: 234) even though there is amismatched base pair (A-C rather than A-T or G-C) at the ninth position.

Conservative substitution: A substitution of an amino acid residue foranother amino acid residue having similar biochemical properties.Typically, conservative substitutions have little to no impact on thebiological activity of a resulting polypeptide. In a particular example,a conservative substitution is an amino acid substitution in a peptidethat does not substantially affect the biological function of thepeptide. A peptide can include one or more amino acid substitutions, forexample 2-10 conservative substitutions, 2-5 conservative substitutions,4-9 conservative substitutions, such as 2, 5 or 10 conservativesubstitutions.

For example, a conservative substitution in a β-chimerin peptide (suchas a peptide encoded by a target sequence associated with SEQ ID NO: 21or 22) does not substantially affect the ability of β-chimerin to conferresistance to HIV infection. In another example, a conservativesubstitution in a Rab9 peptide (such as a peptide encoded by a targetsequence associated with SEQ ID NOS: 118 or 119) is one that does notsubstantially affect the ability of Rab9 to confer resistance toinfection by a pathogen that can hijack a lipid raft, such as HIV orEbola.

A polypeptide can be produced to contain one or more conservativesubstitutions by manipulating the nucleotide sequence that encodes thatpolypeptide using, for example, standard procedures such assite-directed mutagenesis or PCR. Alternatively, a polypeptide can beproduced to contain one or more conservative substitutions by usingstandard peptide synthesis methods. An alanine scan can be used toidentify which amino acid residues in a protein can tolerate an aminoacid substitution. In one example, the biological activity of theprotein is not decreased by more than 25%, for example not more than20%, for example not more than 10%, when an alanine, or otherconservative amino acid (such as those listed below), is substituted forone or more native amino acids.

Examples of amino acids which can be substituted for an original aminoacid in a protein and which are regarded as conservative substitutionsinclude, but are not limited to: Ser for Ala; Lys for Arg; Gln or Hisfor Asn; Glu for Asp; Ser for Cys; Asn for Gin; Asp for Glu; Pro forGly; Asn or Gln for His; Leu or Val for Ile; Ile or Val for Leu; Arg orGln for Lys; Leu or Ile for Met; Met, Leu or Tyr for Phe; Thr for Ser;Ser for Tbr; Tyr for Trp; Trp or Phe for Tyr; and Ile or Leu for Val.

Further information about conservative substitutions can be found in,among other locations in, Ben-Bassat et al., (J. Bacteriol. 169:751-7,1987), O'Regan et al., (Gene 77:237-51, 1989), Sahin-Toth et al.,(Protein Sci. 3:240-7, 1994), Hochuli et al., (Bio/Technology 6:1321-5,1988) and in standard textbooks of genetics and molecular biology.

Ebola virus. A highly contagious hemorrhagic virus named after a riverin the Democratic Republic of the Congo (formerly Zaire) in Africa,where it was first recognized. Ebola is one of two members of a familyof RNA viruses called the Filoviridae. There are four identifiedsubtypes of Ebola virus. Three of the four have caused disease inhumans: Ebola-Zaire, Ebola-Sudan, and Ebola-Ivory Coast. The fourth,Ebola-Reston, has caused disease in nonhuman primates, but not inhumans.

Ebola hemorrhagic fever (Ebola BF) is a severe, often fatal disease inhumans and nonhuman primates (for example, monkeys, gorillas, andchimpanzees) that is caused by Ebola virus infection. Diagnosing EbolaHF in a recently infected individual can be difficult because earlysymptoms, such as red eyes and a skin rash, are nonspecific to the virusand are seen in other subjects with diseases that occur much morefrequently. Antigen-capture enzyme-linked immunosorbent assay (ELISA)testing, IgM ELISA, PCR, and virus isolation can be used to diagnose acase of Ebola HF within a few days after the onset of symptoms. Subjectstested later in the course of the disease, or after recovery, can betested for IgM and IgG antibodies. The disease also can be diagnosedretrospectively in deceased patients by using immunohistochemistrytesting, virus isolation, or PCR.

Encodes: Unless evident from its context, includes DNA sequences thatencode a polypeptide, as the term is typically used, as well as DNAsequences that are transcribed into inhibitory antisense molecules.

Expression: With respect to a gene sequence, refers to transcription ofthe gene and, as appropriate, translation of the resulting mRNA scriptto a protein. Thus, expression of a protein coding sequence results fromtranscription and translation of the coding sequence.

Functional deletion: A mutation, partial or complete deletion,insertion, or other variation made to a gene sequence that inhibitsproduction of the gene product or renders the gene productnon-functional. For example, a functional deletion of a Rab9 gene in acell results in a cells having non-functional Rab9 protein, whichresults in the cell having an increase resistance to infection by apathogen that uses a lipid raft.

Gene. A nucleic acid sequence that encodes a polypeptide under thecontrol of a regulatory sequence, such as a promoter or operator. A geneincludes an open reading frame encoding a polypeptide of the presentdisclosure, as well as exon and (optionally) intron sequences. An intronis a DNA sequence present in a given gene that is not translated intoprotein and is generally found between exons. The coding sequence of thegene is the portion transcribed and translated into a polypeptide (invivo, in vitro or in situ) when placed under the control of anappropriate regulatory sequence. The boundaries of the coding sequencecan be determined by a start codon at the 5′ (amino) terminus and a stopcodon at the 3′ (carboxyl) terminus. If the coding sequence is intendedto be expressed in a eukaryotic cell, a polyadenylation signal andtranscription termination sequence can be included 3′ to the codingsequence.

Transcriptional and translational control sequences include, but are notlimited to, DNA regulatory sequences such as promoters, enhancers, andterminators that provide for the expression of the coding sequence, suchas expression in a host cell. A polyadenylation signal is an exemplaryeukaryotic control sequence. A promoter is a regulatory region capableof binding RNA polymerase and initiating transcription of a downstream(3′ direction) coding sequence. Additionally, a gene can include asignal sequence at the beginning of the coding sequence of a protein tobe secreted or expressed on the surface of a cell. This sequence canencode a signal peptide, N-terminal to the mature polypeptide, whichdirects the host cell to translocate the polypeptide.

Host Cell. Any cell that can be infected with a virus or other pathogen,such as a bacterium. A host cell can be prokaryotic or eukaryotic, suchas a cell from an insect, crustacean, mammal, bird, reptile, yeast, or abacteria such as E. coli. Exemplary host cells include, but are notlimited to, mammalian B-lymphocyte cells. Examples of viruses include,but are not limited to HIV, influenza A, and Ebola.

The host cell can be part of an organism, or part of a cell culture,such as a culture of mammalian cells or a bacterial culture. A hostnucleic acid is a nucleic acid present in a host cell that expresses ahost protein. Decreasing or inhibiting the interaction between a hostpolypeptide or host nucleic acid and a virus or viral protein can occurin vitro, in vivo, and in situ environments.

Human Immunodeficiency Virus (HIV). A retrovirus that causesimmunosuppression in humans and leads to a disease complex known asacquired immunodeficiency syndrome (AIDS). This immunosuppressionresults from a progressive depletion and functional impairment of Tlymphocytes expressing the CD4 cell surface glycoprotein. The loss ofCD4 helper/inducer T cell function may underlie the loss of cellular andhumoral immunity leading to the opportunistic infections andmalignancies seen in AIDS.

Depletion of CD4 T cells results from the ability of HIV to selectivelyinfect, replicate in, and ultimately destroy these T cells (for examplesee Klatzmann et al., Science 225:59, 1984). CD4 itself is an importantcomponent, and in some examples an essential component, of the cellularreceptor for HIV.

HIV subtypes can be identified by particular number, such as HIV-1 andHIV-2. In the HIV life cycle, the virus enters a host cell in at leastthree stages: receptor docking, viral-cell membrane fusion, and particleuptake (D'Souza et al., JAMA 284:215, 2000). Receptor docking beginswith a gp120 component of a virion spike binding to the CD4 receptor onthe host cell. Conformational changes in gp120 induced by gp120-CD4interaction promote an interaction between gp120 and either CCR5 orCXCR4 cellular co-receptors. The gp41 protein then mediates fusion ofthe viral and target cell membranes. More detailed information about HIVcan be found in Coffin et al., Retroviruses (Cold Spring HarborLaboratory Press, 1997).

Hybridization. Hybridization of a nucleic acid occurs when twocomplementary nucleic acid molecules undergo an amount of hydrogenbonding to each other. The stringency of hybridization can varyaccording to the environmental conditions surrounding the nucleic acids,the nature of the hybridization method, and the composition and lengthof the nucleic acids used. For example, temperature and ionic strength(such as Na⁺ concentration) can affect the stringency of hybridization.Calculations regarding hybridization conditions required for attainingparticular degrees of stringency are discussed in Sambrook et al.,Molecular Cloning: A Laboratory Manual (Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., 2001); and Tijssen, LaboratoryTechniques in Biochemistry and Molecular Biology—Hybridization withNucleic Acid Probes Part I, Chapter 2 (Elsevier, N.Y., 1993).

The T_(m) is the temperature at which 50% of a given strand of nucleicacid is hybridized to its complementary strand. The T_(m) of aparticular nucleic acid can be determined by various methods, such asobserving the transition state between a single-stranded anddouble-stranded state during a temperature change, such as heating adsDNA from about 30° C. to about 110° C., and detecting when the dsDNAdenatures to ssDNA. This can be accomplished by determining a meltingprofile for the nucleic acid. For longer nucleic acid fragments, such asPCR products, the nearest-neighbor method can be used to determine T_(m)(Breslauer et al., Proc. Natl. Acad. Sci. USA 83:3746-50, 1986).Additionally, MeltCalc software can be used to determine T_(m) (Schützand von Ahsen, Biotechniques 30:8018-24, 1999).

For purposes of this disclosure, “stringent conditions” encompassconditions under which hybridization only will occur if there is lessthan 25% mismatch between the hybridization molecule and the targetsequence. “Moderate stringency” conditions are those under whichmolecules with more than 25% sequence mismatch will not hybridize;conditions of “medium stringency” are those under which molecules withmore than 15% mismatch will not hybridize, and conditions of “highstringency” are those under which sequences with more than 10% mismatchwill not hybridize. Conditions of “very high stringency” are those underwhich sequences with more than 5% mismatch will not hybridize.

Moderately stringent hybridization conditions are when the hybridizationis performed at about 42° C. in a hybridization solution containing 25mM KPO₄ (pH 7.4), 5×SSC, 5× Denhart's solution, 50 μg/mL denatured,sonicated salmon sperm DNA, 50% formamide, 100% Dextran sulfate, and1-15 ng/mL probe (about 5×10⁷ cpm/μg), while the washes are performed atabout 50° C. with a wash solution containing 2×SSC and 0.1% sodiumdodecyl sulfate.

Highly stringent hybridization conditions are when the hybridization isperformed at about 42° C. in a hybridization solution containing 25 mMKPO₄ (pH 7.4), 5×SSC, 5× Denhart's solution, 50 μg/mL denatured,sonicated salmon sperm DNA, 50% formamide, 10% Dextran sulfate, and 1-15ng/mL probe (about 5×10⁷ cpm/μg), while the washes are performed atabout 65° C. with a wash solution containing 0.2×SSC and 0.1% sodiumdodecyl sulfate.

Infection. The entry, replication, insertion, lysis or other event orprocess involved with the pathogensis of a virus or other infectiousagent into a host cell. Thus, decreasing infection includes decreasingentry, replication, insertion, lysis, or other pathogensis of a virus orother pathogen into a cell or subject, or combinations thereof.Infection includes the introduction of an infectious agent, such as anon-recombinant virus, recombinant virus, plasmid, bacteria, prion,eukaryotic microbe, or other agent capable of infecting a host, such asthe cell of a subject.

In another example, infection is the introduction of a recombinantvector into a host cell via transduction, transformation, transfection,or other method. Vectors include, but are not limited to, viral,plasmid, cosmid, and artificial chromosome vectors. For example, arecombinant vector can include an antisense molecule, RNAi molecule, orsiRNA that recognizes any target sequences associated with SEQ ID NOS:1-227, 229, and 231, or variants, fusions, or fragments thereof, as wellas SEQ ID NOS: 1-227, 229, and 231 themselves.

Influenza virus. A virus that causes respiratory disease or influenza(“the flu”) and can lead to a secondary infection in the host, such as abacterial infection of the lungs. Three types of influenza are currentlyknown: influenza A, influenza B, and influenza C. Influenza A is themost common form of the virus and is capable of infection humans andnon-human animals, such as pigs, horses, chickens, ducks and otherbirds.

The viral genome includes eight RNA molecules. HA, which encodeshemagglutinin (three hemagglutinin subtypes: H1, H2, and H3); M, whichencodes two matrix proteins based on two different open reading frameswithin the nucleic acid sequence; NA encodes for neuraminidase; NPencodes the nucleoprotein; NS encodes two non-structural proteins basedon different open reading frames within the nucleic acid sequence; andthree genes that encode RNA polymerases (PA, PB1, PB2). The influenzavirus can be categorized into subtypes on the bases of the surfaceglycoproteins.

The replication cycle of the influenza virus begins with binding of theviral hemagglutinin molecules to the surface carbohydrate of epithelialcell of a host cell, which draws the virus into the cell byreceptor-mediated endocytosis. The viral membrane fuses with theendocytotic vesicle membrane, allowing the RNA molecules of the viralgenome to enter the interior of the cell where these molecules laterenter the cell nucleus and are replicated into viral-complementary RNAand new viral RNA and transcribed into viral mRNA, which are transportedinto the cytosol where they are translated into the proteins of newviral particles. After viral particles are assembled into new viruses,the neuraminidase glycoproteins proteins aid in the budding of theviruses from the cellular membrane of the host cell, thus releasing newviruses capable of infecting other host cells.

Isolated: An “isolated” biological component (such as a nucleic acid orprotein) has been substantially separated, produced apart from, orpurified away from other biological components in the cell of theorganism in which the component naturally occurs, such as otherchromosomal and extrachromosomal DNA and RNA, and proteins. Nucleicacids and proteins which have been “isolated” include nucleic acids andproteins purified by standard purification methods. The term alsoembraces nucleic acids and proteins prepared by recombinant expressionin a host cell as well as chemically synthesized nucleic acids, proteinsand peptides.

Nucleic acid. A deoxyribonucleotide or ribonucleotide polymer in eithersingle (ss) or double stranded (ds) form, and can include analogues ofnatural nucleotides that hybridize to nucleic acids in a manner similarto naturally occurring nucleotides. In some examples, a nucleic acid isa nucleotide analog.

Unless otherwise specified, any reference to a nucleic acid moleculeincludes the reverse complement of nucleic acid. Except wheresingle-strandedness is required by the text herein (for example, a ssRNAmolecule), any nucleic acid written to depict only a single strandencompasses both strands of a corresponding double-stranded nucleicacid. For example, depiction of a plus-strand of a dsDNA alsoencompasses the complementary minus-strand of that dsDNA. Additionally,reference to the nucleic acid molecule that encodes a specific protein,or a fragment thereof, encompasses both the sense strand and its reversecomplement.

In particular examples, a nucleic acid includes a nucleotide sequenceshown in any of SEQ ID NOS: 1-227, 229, and 231, or a variant, fragment,or fusion thereof. In other examples, a nucleic acid has a nucleotidesequence including a target sequence associated with SEQ ID NOS: 1-227,229, and 231, or a variant, fragment, or fusion thereof, such as thecorresponding cDNA or mRNA of SEQ ID NOS: 1-227, 229, and 231.

The fragment can be any portion of the nucleic acid corresponding to atleast 5 contiguous bases from any target nucleic acid sequenceassociated with SEQ ID NOS: 1-227, 229, and 231, for example at least 20contiguous bases, at least 50 contiguous bases, at least 100 contiguousbases, at least 250 contiguous bases, or even at least 500 or morecontiguous bases. A fragment can be chosen from a particular portion ofany of the target sequences associated with SEQ ID NOS: 1-227, 229, and231, such as a particular half, third, fourth, fifth, sixth, seventh,eighth, ninth, tenth, or smaller portion of any of the target sequencesassociated with SEQ ID NOS: 1-227, 229, and 231. Fragments of thenucleic acids described herein can be used as probes and primers.

Oligonucleotide. A linear polynucleotide (such as DNA or RNA) sequenceof at least 9 nucleotides, for example at least 15, 18, 24, 25, 30, 50,100, 200 or even 500 nucleotides long. In particular examples, anoligonucleotide is about 6-50 bases, for example about 10-25 bases, suchas 12-20 bases.

An oligonucleotide analog refers to moieties that function similarly tooligonucleotides, but have non-naturally occurring portions. Forexample, oligonucleotide analogs can contain non-naturally occurringportions, such as altered sugar moieties or inter-sugar linkages, suchas a phosphorothioate oligodeoxynucleotide. Functional analogs ofnaturally occurring polynucleotides can bind to RNA or DNA, and includepeptide nucleic acid (PNA) molecules.

Open reading frame (ORF). A series of nucleotide triplets (codons)coding for amino acids without any internal termination codons. Thesesequences are usually translatable into a peptide.

Operably linked. A first nucleic acid sequence is operably linked with asecond nucleic acid sequence when the first nucleic acid sequence isplaced in a functional relationship with the second nucleic acidsequence. For instance, a promoter is operably linked to a codingsequence if the promoter affects the transcription or expression of thecoding sequence. Generally, operably linked DNA sequences are contiguousand, where necessary to join two protein coding regions, in the samereading frame.

Pathogen: A disease-producing agent. Examples include, but are notlimited to viruses, bacteria, and fungi.

Pharmaceutical agent or drug: A chemical compound or composition capableof inducing a desired therapeutic or prophylactic effect whenadministered to a subject, alone or in combination with anothertherapeutic agent(s) or pharmaceutically acceptable carriers. In aparticular example, a pharmaceutical agent decreases or even inhibitsinfection of a cell, such as the cell of a subject, by a pathogen, suchas a virus.

Polymorphism. A polymorphism exists when two or more versions of anucleic acid sequence exist within a population of subjects. Forexample, a polymorphic nucleic acid can be one where the most commonallele has a frequency of 99% or less. Different alleles can beidentified according to differences in nucleic acid sequences, andgenetic variations occurring in more than 1% of a population (which isthe commonly accepted frequency for defining polymorphism) are usefulpolymorphisms for certain applications.

The allelic frequency (the proportion of all allele nucleic acids withina population that are of a specified type) can be determined by directlycounting or estimating the number and type of alleles within apopulation. Polymorphisms and methods of determining allelic frequenciesare discussed in Hartl, D. L. and Clark, A. G., Principles of PopulationGenetics, Third Edition (Sinauer Associates, Inc., Sunderland Mass.,1997), particularly in chapters 1 and 2.

Preventing or treating a disease: “Preventing” a disease refers toinhibiting the full development of a disease, for example preventingdevelopment of a viral infection. “Treatment” refers to a therapeuticintervention that ameliorates a sign or symptom of a disease orpathological condition related to a viral infection, such as inhibitingor decreasing viral infection.

Probes and primers. A probe includes an isolated nucleic acid attachedto a detectable label or other reporter molecule. Typical labelsinclude, but are not limited to radioactive isotopes, enzyme substrates,co-factors, ligands, chemiluminescent or fluorescent agents, haptens,and enzymes. Methods for labeling and guidance in the choice of labelsappropriate for various purpose are discussed for example in Sambrook etal. (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y.,1989) and Ausubel et al. (In Current Protocols in Molecular Biology,John Wiley & Sons, New York, 1998).

Primers are short nucleic acid molecules, such as DNA oligonucleotidesten nucleotides or more in length. Longer DNA oligonucleotides can beabout 15, 20, 25, 30 or 50 nucleotides or more in length. Primers can beannealed to a complementary target DNA strand by nucleic acidhybridization to form a hybrid between the primer and the target DNAstrand, and then the primer extended along the target DNA strand by aDNA polymerase enzyme. Primer pairs can be used for amplification of anucleic acid sequence, for example by the polymerase chain reaction(PCR) or other nucleic-acid amplification methods.

Nucleic acid probes and primers can be prepared based on the nucleicacid molecules of the target sequences associated with SEQ ID NOS:1-227, 229, and 231, as indicators of resistance to infection. Probesand primers can be based on fragments or portions of these nucleic acidmolecules, or on the reverse complement of these sequences, as well asprobes and primers to 5′ or 3′ regions of the nucleic acids.

The specificity of a probe or primer increases with its length. Thus,for example, a primer that includes 30 consecutive nucleotides of aβ-chimerin or Rab9 gene will anneal to a target sequence, such asanother homolog of a β-chimerin or Rab9 gene, respectively, with ahigher specificity than a corresponding primer of only 15 nucleotides.Thus, to obtain greater specificity, probes and primers can be selectedthat include at least 20, 25, 30, 35, 40, 45, 50 or more consecutivenucleotides of a nucleic acid disclosed herein.

Protein coding sequence or a sequence that encodes a peptide: A nucleicacid sequence that is transcribed (in the case of DNA) and is translated(in the case of mRNA) into a peptide in vitro or in vivo when placedunder the control of appropriate regulatory sequences. The boundaries ofthe coding sequence are determined by a start codon at the 5′ (amino)terminus and a translation stop codon at the 3′ (carboxy) terminus. Acoding sequence can include, but is not limited to, cDNA fromprocaryotic or eukaryotic mRNA, genomic DNA sequences from procaryoticor eukaryotic DNA, and even synthetic DNA sequences. A transcriptiontermination sequence is usually be located 3′ to the coding sequence.

Purified. The term purified does not require absolute purity; rather, itis a relative term. Thus, for example, a purified peptide preparation isone in which the peptide or protein is more enriched than the peptide orprotein is in its environment within a cell, such that the peptide issubstantially separated from cellular components (nucleic acids, lipids,carbohydrates, and other polypeptides) that may accompany it. In anotherexample, a purified peptide preparation is one in which the peptide issubstantially-free from contaminants, such as those that might bepresent following chemical synthesis of the peptide.

In one example, an peptide is purified when at least 60% by weight of asample is composed of the peptide, for example when 75%, 95%, or 99% ormore of a sample is composed of the peptide, such as a β-chimerin orRab9 peptide. Examples of methods that can be used to purify proteins,include, but are not limited to the methods disclosed in Sambrook et al.(Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., 1989,Ch. 17). Protein purity can be determined by, for example,polyacrylamide gel electrophoresis of a protein sample, followed byvisualization of a single polypeptide band upon staining thepolyacrylamide gel; high-pressure liquid chromatography; sequencing; orother conventional methods.

Rab9: The term Rab9 includes any Rab9 gene, cDNA, RNA, or protein fromany organism and that is a Rab9 that can transport late endosomes totrans-golgi and function as a ras-like GTPase. In some examples, Rab9 isinvolved in lipid raft formation.

Examples of native Rab9 nucleic acid sequences include, but are notlimited to, target sequences associated with SEQ ID NOS: 118 and 119.Examples of Rab9 amino acid sequences include, but arm not limited to:Genbank Accession Nos: BC017265.2 and NM_(—)004251.3 (cDNA) as well asP51151 and AAH17265 (proteins). In one example, a Rab9 sequence includesa full-length wild-type (or native) sequence, as well as Rab9 allelicvariants, variants, fragments, homologs or fusion sequences that retainthe ability to transport late endosomes to trans-golgi. In certainexamples, Rab9 has at least 80% sequence identity, for example at least85%, 90%, 95%, or 98% sequence identity to a native Rab9.

In other examples, Rab9 has a sequence that hybridizes to a sequence setforth in GenBank Accession No. BC017265.2 or NM_(—)004251.3, and retainsRab9 activity.

Recombinant. A recombinant nucleic acid or protein is one that has asequence that is not naturally occurring or has a sequence that is madeby an artificial combination of two otherwise separated segments ofsequence. This artificial combination can be accomplished, for example,by chemical synthesis or by the artificial manipulation of isolatedsegments of nucleic acids or proteins, for example, by geneticengineering techniques.

RNA interference (RNAi): A post-transcriptional gene silencing mechanismmediated by double-stranded RNA (dsRNA). Introduction of dsRNA intocells, such as RNAi compounds or siRNA compounds, induces targeteddegradation of RNA molecules with homologous sequences. RNAi compoundsare typically longer than an siRNA molecule. For example, an RNAimolecule can be at least about 25 nucleic acids, at least about 27nucleic acids, or even at least about 400 nucleotides in length.

RNAi compounds can be used to modulate transcription, for example, bysilencing genes, such as Rab9, β-chimerin, or combinations thereof. Incertain examples, an RNAi molecule is directed against a certain targetgene, such as Rab9, β-chimerin, or combinations thereof, and is used todecrease viral infection.

Sequence identity: The similarity between nucleic acid or amino acidsequences is expressed in terms of the similarity between the sequences.Sequence identity is frequently measured in terms of percentage identity(or similarity or homology); the higher the percentage, the more similarthe two sequences are. Homologs or variants of a protein or nucleic aciddisclosed herein, such as target sequences associated with SEQ ID NOS:1-232, and their corresponding cDNA and protein sequences, will possessa relatively high degree of sequence identity when aligned usingstandard methods.

Methods of alignment of sequences for comparison are well known in theart. Various programs and alignment algorithms are described in: Smithand Waterman, Adv. Appl. Math. 2:482, 1981; Needleman and Wunsch, J.Mol. Biol. 48:443, 1970; Pearson and Lipman, Proc. Natl. Acad. Sci.U.S.A. 85:2444, 1988; Higgins and Sharp, Gene 73:237-44, 1988; Higginsand Sharp, CABIOS 5:151-3, 1989; Corpet et al., Nucl. Acids Res.16:10881-90, 1988; Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A.85:2444, 1988; and Altschul et al., Nature Genet. 6:119-29, 1994.

The NCBI Basic Local Alignment Search Tool (BLAST™) (Altschul et al., J.Mol. Biol. 215:403-10, 1990) is available from several sources,including the National Center for Biotechnology Information (NCBI,Bethesda, Md.) and on the Internet, for use in connection with thesequence analysis programs blastp, blastn, blastx, tblastn and tblastx.

Variants of a peptide, such as a peptide encoded by any target sequenceassociated with SEQ ID NOS: 1-227, 229, and 231, as well as any targetsequence associated with SEQ ID NOS: 228, 230, and 232, are typicallycharacterized by possession of at least 70% sequence identity countedover the full length alignment with the amino acid sequence encoded byany target sequence associated with SEQ ID NOS: 1-227, 229, or 231,using the NCBI Blast 2.0, gapped blastp set to default parameters. Forcomparisons of amino acid sequences of greater than about 30 aminoacids, the Blast 2 sequences function is employed using the defaultBLOSUM62 matrix set to default parameters, (gap existance cost of 11,and a per residue gap cost of 1). When aligning short peptides (fewerthan around 30 amino acids), the alignment is performed using the Blast2 sequences function, employing the PAM30 matrix set to defaultparameters (open gap 9, extension gap 1 penalties). Proteins with evengreater similarity to the reference sequences will show increasingpercentage identities when assessed by this method, such as at least80%, at least 90%, at least 95%, at least 98%, or even at least 99%sequence identity. When less than the entire sequence is being comparedfor sequence identity, homologs and variants will typically posses atleast 80% sequence identity over short windows of 10-20 amino acids, andmay possess sequence identities of at least 85%, at least 90%, at least95%, or at least 98% depending on their similarity to the referencesequence. Methods for determining sequence identity over such shortwindows are described at the website that is maintained by the NationalCenter for Biotechnology Information in Bethesda, Md. One of skill inthe art will appreciate that these sequence identity ranges are providedfor guidance only; it is entirely possible that strongly significanthomologs could be obtained that fall outside of the ranges provided.

Similar methods can be used to determine the sequence identity betweentwo or more nucleic acids. To compare two nucleic acid sequences, theBLASTN options can be set as follows: −i is set to a file containing thefirst nucleic acid sequence to be compared (such as C:\seq1.txt); −j isset to a file containing the second nucleic acid sequence to be compared(such as C:\seq2.txt); −p is set to blastn; −o is set to any desiredfile name (such as C:\output.txt); −q is set to −1; −r is set to 2; andall other options are left at their default setting. For example, thefollowing command can be used to generate an output file containing acomparison between two sequences: C:\B12seq −i c:\seq1.txt −jc:\seq2.txt −p blastn −o c:\output.txt −q −1 −r 2.

Once aligned, the number of matches is determined by counting the numberof positions where an identical nucleotide or amino acid residue ispresented in both sequences. The percent sequence identity is determinedby dividing the number of matches either by the length of the sequenceset forth in the identified sequence, or by an articulated length (forexample, 100 consecutive nucleotides or amino acid residues from asequence set forth in an identified sequence), followed by multiplyingthe resulting value by 100. For example, a nucleic acid sequence thathas 1166 matches when aligned with a test sequence having 1154nucleotides is 75.0 percent identical to the test sequence (for example,1 166+1554*100=75.0). The percent sequence identity value is rounded tothe nearest tenth. For example, 75.11, 75.12, 75.13, and 75.14 arerounded down to 75.1, while 75.15, 75.16, 75.17, 75.18, and 75.19 arerounded up to 75.2. The length value will always be an integer. Inanother example, a target sequence containing a 20-nucleotide regionthat aligns with 20 consecutive nucleotides from an identified sequenceas follows contains a region that shares 75 percent sequence identity tothat identified sequence (for example, 15+20*100=75).      1                  20 Target Sequence: AGGTCGTGTACTGTCAGTCA      | || ||| |||| |||| | Identified Sequence: ACGTGGTGAACTGCCAGTGA

The nucleic acids disclosed herein include nucleic acids have nucleotidesequences that are at least 70%, at least 75%, at least 80%, at least85%, at least 90%, at least 95%, at least 98%, or at least 99% identicalto the nucleotide sequence of any target sequence associated with SEQ IDNOS: 1-227, 229, and 231. In particular examples, a nucleic acid issubstantially similar to the nucleotide sequence of any target sequenceassociated with SEQ ID NOS: 1-227, 229, and 231. A first nucleic acid is“substantially similar” to a second nucleic acid if, when the firstnucleic acid is optimally aligned (with appropriate nucleotide deletionsor gap insertions) with the second nucleic acid (or its complementarystrand) and there is nucleotide sequence identity of at least about 90%,for example at least about 95%, at least 98% or at least 99% identity.An alternative indication that two nucleic acid molecules are closelyrelated is that the two molecules hybridize to each other understringent conditions.

Nucleic acid sequences that do not show a high degree of identity maynevertheless encode similar amino acid sequences, due to the degeneracyof the genetic code. It is understood that changes in nucleic acidsequence can be made using this degeneracy to produce multiple nucleicacid molecules that all encode substantially the same protein.

Short interfering or interrupting RNA (siRNA). Double-stranded RNAs thatcan induce sequence-specific post-transcriptional gene silencing,thereby decreasing or even inhibiting gene expression. In some examples,siRNA molecules are about 19-23 nucleotides in length, such as at least21 nucleotides, for example at least 23 nucleotides.

In one example, siRNA triggers the specific degradation of homologousRNA molecules, such as mRNAs, within the region of sequence identitybetween both the siRNA and the target RNA. For example, WO 02/44321discloses siRNAs capable of sequence-specific degradation of targetmRNAs when base-paired with 3′ overhanging ends. The direction of dsRNAprocessing determines whether a sense or an antisense target RNA can becleaved by the produced siRNA endonuclease complex. Thus, siRNAs can beused to modulate transcription, for example, by silencing genes, such asRab9, β-chimerin, or combinations thereof. The effects of siRNAs havebeen demonstrated in cells from a variety of organisms, includingDrosophila, C. elegans, insects, frogs, plants, fungi, mice and humans(for example, WO 02/44321; Gitlin et al., Nature 418:430-4, 2002; Caplenet al., Proc. Natl. Acad. Sci. 98:9742-9747, 2001; and Elbashir et al.,Nature 411:494-8, 2001).

In certain examples, siRNAs are directed against certain target genes,such as Rab9, β-chimerin, or combinations thereof, to confirm results ofthe gene-trap method used against the same nucleic acid sequence.

Specific binding agent. An agent that binds substantially only to adefined target. For example, a protein-specific binding agent bindssubstantially only the specified protein and a nucleic acid specificbinding agent binds substantially only the specified nucleic acid.

As used herein, the term “protein [X]specific binding agent” includesanti-[X] protein antibodies (including polyclonal or monoclonalantibodies and functional fragments thereof) and other agents (such assoluble receptors) that bind substantially only to the [X]protein. Inthis context, [X]refers to any specific or designated protein, forinstance β-chimerin, Rab9, or any protein listed in Table 1 or encodedby a target sequence associated with SEQ ID NOS: 1-227, 229, and 231(including variants, fragments, and fusions thereof).

Anti-[X] protein antibodies can be produced using standard proceduressuch as those described in Harlow and Lane (Using Antibodies: ALaboratory Manual, Cold Spring Harbor Laboratory Press: Cold SpringHarbor, 1998). Antibodies can be polyclonal or monoclonal antibodies,humanized antibodies, Fab fragments, F(ab′)2 fragments, single chainantibodies, or chimeric antibodies. For example, polyclonal antibodiescan be produced by immunizing a host animal by injection withpolypeptides described herein, including the target sequences associatedwith SEQ ID NOS: 1-227, 229, 231 (or variants, fragments, or fusionsthereof). The production of monoclonal antibodies can be accomplished bya variety of methods, such as the hybridoma technique (Kohler andMilstein, Nature 256:495-7, 1975), the human B-cell technique (Kosbor etal., Immunology Today 4:72, 1983), or the EBV-hybridoma technique (Coleet al., in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc.,pp. 77-96, 1983). Additionally, chimeric antibodies can be produced (forexample, see Morrison et al., J. Bacteriol. 159:870, 1984; Neuberger etal., Nature 312:604-8, 1984; and Takeda et al., Nature 314:452-4, 1985),as well as single-chain antibodies (for example, see U.S. Pat. Nos.5,476,786; 5,132,405; and 4,946,778).

The determination that a particular agent binds substantially only tothe specified protein readily can be made by using or adapting routineprocedures. For example, Western blotting can be used to determine thata given protein binding agent, such as an anti-[X] protein monoclonalantibody, binds substantially only to the [X] protein. Other assaysinclude, but are not limited to, competitive and non-competitivehomogenous and heterogeneous enzyme-linked immunosorbent assays (ELISA)as symmetrical or asymmetrical direct or indirect detection formats;“sandwich” immunoassays; immunodiffusion assays; in situ immunoassays(for example, using colloidal gold, enzyme or radioisotope labels);agglutination assays; complement fixing assays; immunoelectrophorecticassays; enzyme-linked immunospot assays (ELISPOT); radioallergosorbenttests (RAST); fluorescent tests, such as used in fluorescent microscopyand flow cytometry; Western, grid, dot or tissue blots; dip-stickassays; halogen assays; or antibody arrays (for example, see O'Meara andTovey, Clin. Rev. Allergy Immunol., 18:341-95, 2000; Sambrook et al.,2001, Appendix 9; Simonnet and Guilloteau, in: Methods of ImmunologicalAnalysis, Masseyeff et al. (Eds.), VCH, New York, 1993, pp. 270-388).

A specific binding agent also can be labeled for direct detection (seeChapter 9, Harlow and Lane, Antibodies: A Laboratory Manual. 1988).Suitable labels include (but are not limited to) enzymes (such asalkaline phosphatase (AP) or horseradish peroxidase (HRP)), fluorescentlabels, colorimetric labels, radioisotopes, chelating agents, dyes,colloidal gold, ligands (such as biotin), and chemiluminescent agents.

Shorter fragments of antibodies can also serve as specific bindingagents. For instance, Fabs, Fvs, and single-chain Fvs (SCFvs) that bindto a specified protein would be specific binding agents. These antibodyfragments include: (1) Fab, the fragment containing a monovalentantigen-binding fragment of an antibody molecule produced by digestionof whole antibody with the enzyme papain to yield an intact light chainand a portion of one heavy chain; (2) Fab′, the fragment of an antibodymolecule obtained by treating whole antibody with pepsin, followed byreduction, to yield an intact light chain and a portion of the heavychain; two Fab′ fragments are obtained per antibody molecule; (3)(Fab′)2, the fragment of the antibody obtained by treating wholeantibody with the enzyme pepsin without subsequent reduction; (4)F(ab)2, a dimer of two Fab′ fragments held together by two disulfidebonds; (5) Fv, a genetically engineered fragment containing the variableregion of the light chain and the variable region of the heavy chainexpressed as two chains; and (6) single chain antibody (“SCA”), agenetically engineered molecule containing the variable region of thelight chain, the variable region of the heavy chain, linked by asuitable polypeptide linker as a genetically fused single chainmolecule. Methods of malting these fragments are routine. For example,construction of Fab expression libraries permits the rapid and easyidentification of monoclonal Fab fragments with the desired specificityfor a protein described herein.

Subject: Living multi-cellular vertebrate organisms, including human andveterinary subjects, such as cows, pigs, horses, dogs, cats, birds,reptiles, and fish.

Target sequences associated with SEQ ID NO: When used herein, thisphrase refers to any nucleic acid sequence, amino acid sequence, orcombination of nucleic acid and amino acid sequences, that are involvedin viral infection, and therefore serve as targets for inhibiting viralinfection, and which are or include a specified SEQ ID NO, are involvedin the expression of the SEQ ID NO, or are peptide (including protein)sequences that are expressed by such specified SEQ ID NO. Although atarget sequence may refer to a SEQ ID NO of a sequence obtained from aparticular species, the target sequences also include homologues of thesequence from other related species, such as other mammals. For example,the phrase “target sequences associated with SEQ ID NO. X” can refer tothe entire gene sequence of which the particular SEQ ID NO X is a part,the appropriate coding sequence, a promoter sequence associated with thegene, or the corresponding protein sequence, as well as variants,fragments, homologues, and fusions thereof that retain the activity ofthe native sequence.

For example, when using the phrase “sequences associated with SEQ IDNOS: 21-22,” this term encompases β-chimerin genomic sequences,endogenous promoter sequences that promote the expression of β-chimerin,coding sequences, and β-chimerin proteins, as well as variants,fragments homologues and fusions thereof that retain the activity of thenative sequence. A particular cDNA sequence associated with SEQ ID NOS:21-22 is provided in GenBank Accession No. NM_(—)004067, and aparticular protein sequence associated with SEQ ID NOS: 21-22 isprovided in NP_(—)004058.1.

The term “a GenBank Accession No. associated with SEQ ID NO. X” refersto a GenBank Accession No. that includes SEQ ID NO. X, or is a homologof SEQ ID NO: X from another mammal, for example a human homolog. TheGenBank Accession No. may, in some examples, also identify a codingsequence of an open reading frame, and the sequence of the proteinencoded by SEQ ID NO. X.

Although sequences are provided herein that encode (or are includedwithin sequences that encode) host proteins that are involved in viralinfection, it should be understood that the ultimate goal is tointerfere with the activity of the protein that has been identified tobe involved in viral pathogenesis. Such interference can be at eitherthe level of the nucleic acid that encodes the protein (for example byreducing or otherwise disrupting expression of the protein), or at thelevel of the protein itself (for example by interfering with theactivity of the protein, or its interaction with the virus). Thedisclosure of specific techniques for achieving these goals inparticular species should not be interpreted to limit the method tothese particular techniques, or to particular species in which the viralinteraction is first identified. The identification of the viralinteraction in one species indicates the importance of the interactionbetween the virus and the protein in that species, as well as theinteraction of the virus with homologues of that protein in otherspecies.

Target sequence of a nucleic acid: A portion of a nucleic acid that,upon hybridization to a therapeutically effective oligonucleotide oroligonucleotide analog, results in reduction or even inhibition ofinfection by an infectious agent. An antisense or a sense molecule canbe used to target a portion of dsDNA, since either can interfere withthe expression of that portion of the dsDNA. The antisense molecule canbind to the plus strand, and the sense molecule can bind to the minusstrand. Thus, target sequences can be ssDNA, dsDNA, and RNA.

Therapeutically active molecule: An agent, such as a protein, antibodyor nucleic acid, that can decrease expression of a host protein involvedin viral infection (such as those listed in Table 1 or target sequencesassociated with any of SEQ ID NOS: 1-232, or can decrese an interactionbetween a host protein involved in viral infection and a viral protein,such as HIV, Ebola, or influenza A, as measured by clinical response(for example, a decrease in infection by a virus, such as an inhibitionof infection). Therapeutically active agents also include organic orother chemical compounds that mimic the effects of the therapeuticallyeffective peptide or nucleic acids.

Therapeutically Effective Amount: An amount of a pharmaceuticalpreparation that alone, or together with an additional therapeuticagent(s), induces the desired response. The preparations disclosedherein arm administered in therapeutically effective amounts.

In one example, a desired response is to decrease or inhibit viralinfection of a cell, such as a cell of a subject. Viral infection doesnot need to be completely inhibited for the pharmaceutical preparationto be effective. For example, a pharmaceutical preparation can decreaseviral infection by a desired amount, for example by at least 20%, atleast 50%, at least 60%, at least 70%, at least 80%, at least 90%, atleast 95%, at least 98%, or even at least 100%, as compared to an amountof viral infection in the absence of the pharmaceutical preparation.This decrease or inhibition can result in halting or slowing theprogression of, or inducing a regression of a pathological conditioncaused by the viral infection, or which is capable of relieving signs orsymptoms caused by the condition.

In another or additional example, it is an amount sufficient topartially or completely alleviate symptoms of viral infection within ahost subject. Treatment can involve only slowing the progression of theinfection temporarily, but can also include halting or reversing theprogression of the infection permanently.

Effective amounts of the therapeutic agents described herein can bedetermined in many different ways, such as assaying for a reduction inthe rate of infection of cells or subjects, a reduction in the viralload within a host, improvement of physiological condition of aninfected subject, or increased resistance to infection followingexposure to the virus. Effective amounts also can be determined throughvarious in vitro, in vivo or in situ assays, including the assaysdescribed herein.

The disclosed therapeutic agents can be administered in a single dose,or in several doses, for example daily, during a course of treatment.However, the effective amount of can be dependent on the source applied(for example a nucleic acid isolated from a cellular extract versus achemically synthesized and purified nucleic acid), the subject beingtreated, the severity and type of the condition being treated, and themanner of administration. In addition, the disclosed therapeutic agentscan be administered alone, or in the presence of a pharmaceuticallyacceptable carrier, or in the presence of other therapeutic agents, forexample other anti-viral agents.

Transduced and Transformed: A virus or vector “transduces” or“transfects” a cell when it transfers nucleic acid into the cell. A cellis “transformed” by a nucleic acid transduced into the cell when the DNAbecomes stably replicated by the cell, either by incorporation of thenucleic acid into the cellular genome, or by episomal replication. Asused herein, the term transformation encompasses all techniques by whicha nucleic acid molecule might be introduced into such a cell, includingtransfection with viral vectors, transformation with plasmid vectors,and introduction of naked DNA by electroporation, lipofection, andparticle gun acceleration.

Transfected: A transfected cell is a cell into which has been introduceda nucleic acid molecule by molecular biology techniques. The termtransfection encompasses all techniques by which a nucleic acid moleculecan be introduced into such a cell, including transfection with viralvectors, transformation with plasmid vectors, and introduction of nakedDNA by electroporation, lipofection, and particle gun acceleration.

Transgene: An exogenous nucleic acid sequence supplied by a vector. Inone example, a transgene includes any target sequence associated withSEQ ID NOS: 1-227, 229, 231 (or variants, fragments, or fusionsthereof), for example a nucleic acid that encodes a beta-chimerin orRab9.

Variants, fragments or fusions: The disclosed nucleic acid sequences,such as target sequences associated with SEQ ID NOS: 1-227, 229, and231, and the proteins encoded thereby, include variants, fragments, andfusions thereof that retain the native biological activity (such asplaying a role in viral infection). DNA sequences which encode for aprotein or fusion thereof, or a fragment or variant of thereof can beengineered to allow the protein to be expressed in eukaryotic cells ororganisms, bacteria, insects, and/or plants. To obtain expression, theDNA sequence can be altered and operably linked to other regulatorysequences. The final product, which contains the regulatory sequencesand the therapeutic protein, is referred to as a vector. This vector canbe introduced into eukaryotic, bacteria, insect, and/or plant cells.Once inside the cell the vector allows the protein to be produced.

One of ordinary skill in the art will appreciate that the DNA can bealtered in numerous ways without affecting the biological activity ofthe encoded protein. For example, PCR can be used to produce variationsin the DNA sequence which encodes a protein. Such variants can bevariants optimized for codon preference in a host cell used to expressthe protein, or other sequence changes that facilitate expression.

Vector: A nucleic acid molecule as introduced into a host cell, therebyproducing a transformed host cell. A vector can include nucleic acidsequences that permit it to replicate in a host cell, such as an originof replication, and can also include one or more selectable marker genesand other genetic elements. An insertional vector is capable ofinserting itself into a host nucleic acid. For example, recombinantlambda-phage vectors of host genomes (Coffin et al., Retroviruses,Chapter 5).

Wild-type. A naturally occurring, non-mutated version of a nucleic acidsequence. Among multiple alleles, the allele with the greatest frequencywithin the population is usually (but not necessarily) the wild-type.The term “native” can be used as a synonym for “wild-type.”

Nucleic Acids and Proteins Involved in Viral Infection

Examples of host nucleic acids and proteins that play a role in viralinfection have been identified and are summarized in Table 1. Thesenucleic acids and proteins offer new targets for therapies that reduceor even inhibit or prevent viral infection, and offer new strategies forassessing the risk of infection among certain populations. While thetarget genes were identified in an assay using the recited virus, it isappreciated that infections agents such as viruses will share commonpathways. Thus, the host sequences set forth below can be interferedwith to decrease infection in a host cell.

Examples of viruses that can be inhibited are described in Virology,Volumes 1 and 2 by Bernard Fields, Second Edition, 1990, Raven Press.Exemplary viruses include, but are not limited to members of the family:Picornaviridae (such as Poliovirus, Coxsackievirus, Echovirus,Rhinovirus, and Hepatitis A and E); Calciviridae (such as Norwalk andrelated viruses); Togaviridae and Flavivirdae (such as hepatitis C,Alphavirus, and Rubella); Coronaviridae (such as SARS); Rhabdoviridae(such as Rabies); Filoviridae (such as Marburg and Ebola);Paramyxoviridae (such as Parainfluenza, Mumps, Measles, Hydra andRespiratory Synctial virus); Orthomyxoviridae; Bunyaviridae (includingall subtypes and strains); Arenaviridae (such as lymphocyticchoreomeningitis virus and lassa fever and related viruses); Reoviridae(such as Reovirus and Rotavirus); Retroviridae (such as HTLV, HIV, andLentivirus); Papoviridae (such as Polyoma and Papilloma); Adenoviridae(such as Adenovirus); Parvoviridae (such as Parvovirus); Herpesviridae(such as Herpes 1 and 2, Cytomegalovirus, Varicella-Zoster, Kaposisarcoma related virus (HHV9), Epstein Barr Virus, and HHV6.7(roseolavirus)); Poxviridae (such as Pox); Hepadnaviridae (such asHepatitis B); as well as Hepatitis D virus, Hanta virus, and newlyidentified infectious agents. TABLE 1 Examples of Host Genes andProtlens Implicated in Pathogenesis GenBank Accession Nos Associated SEQID for cDNA and Nucleic Acid or Protein Virus NO: Protein T-cellreceptor V beta chain HIV 1-19 T-cell receptor V-D-J beta 2.1 chain HIV20 β-chimerin (CHN2) HIV 21-22 NM_004067; NP_004058.1 Malic enzyme 1(ME1) HIV and 23 BC025246; Influenza A AAH25246.1 Hypothetical proteinXP_174419 HIV and 24 Influenza A sequence from Chromosome 4q31.3-32 HIVand 25-27 Influenza A alpha satellite DNA HIV 28 LOC2537888 andLOC219938; coagulation HIV 29 factor III (F3) and LOC91759 similar toKOX4 (LOC131880) and HIV 30 LOC166140 LOC222474 and similar to Rhoguanine HIV 31 nucleotide exchange factor 4, isoform a, APC-stimulatedguanine nucleotide exchange factor (LOC221178); T-cell receptor betaribosomal protein L7A-like 4 (RPL7ALA) HIV 32 and v-src sarcoma(Schmidt-Ruppin A-2) viral oncogene homolog (avian) (SRC) KIAA0564 HIV33 alpha satellite DNA; M96 protein HIV 34 hypothetical protein similarto G proteins, HIV 35 especially RAP-2A (LOC57826); LOC161005 andosteoblast specific factor 2 (fasciclin I-like; OSF-2) Canis familiarisT-cell leukemia Influenza A 36-37 translocation-associated (TCTA) gene,aminomethyltransferase (AMT) gene, dystroglycan (DAG1) gene, and bassoon(BSN) gene LIM domain containing preferred Influenza A 38-48translocation partner in lipoma (LPP) sequence between LOC253121 andInfluenza A 49 hyaluronan synthase 2 (HAS2) Testin 2 and Testin 3 (TES)Influenza A 50-57 PTPN1 gene for protein tyrosine Influenza A 58-59phosphatase, non-receptor type 1 sequence between LOC149360 andInfluenza A 60 LOC253961 sequence between KIAA 1560 and TectorinInfluenza A 61 beta (TECTB) Cadherin related 23 (CDH23) Influenza A 62BC032581; AAH32581.1 Mycloid/lyniphoma or mixed lineage Influenza A 63leukemia, translocated to 10 (MMLT10) exportin 5 (XPO5) and DNApolymerase Ebola eta (POLH) heterogenous nuclear riboprotein C Ebola67-75 (C1/C2) (HNRPC) alpha-endosulfine pseudogene (ENSAP) Ebola 76 andLOC128741 LOC222888 Ebola 77 LOC138421 and zinc finger protein 297BEbola 78 (ZNF297B) sideroflexin 5 (SFXN5) Ebola 79 AY044437; AAK95826importin 9 (FLJ10402) Ebola 80 T-cell receptor beta Ebola 81-82 similarto murine putative transcription Ebola 83-99 factor ZNFI3l (LOC 135952)KIAA1259 Ebola 100-101 AB033085; NP_115572 MURRI and CCT4 Ebola 102FLJ40773 and similar to ribosonial protein Ebola 103 L24-like(LOC149360) Testin 2 slid 3 (TES) Ebola 104-107 See abovepolybromol(PB1) Ebola 108 NM_018165.2; NP_060635 DNA damage inducibletranscript 3 Ebola 109 PDZ and LIM domain 1 (elfin) (PDLIM1) Ebola 110LOC284803 Ebola 111-112 PRO0097 and FLJ31958 Ebola 113 small induciblecytokine E, member 1 Ebola 114-116 (endothelial monocyte-activating)(SCYE1) E3 ubiquitin ligase (SMURF2) and Ebola 117-119 MGC40489 Rasoncogene family member Rab9 Ebola 118-119 PRO1617 and retinoblastoniabinding Ebola 120-122 NM_000321; protein 1 (RBBP1) NP_000312.1 region ofchromosome 2q12 Ebola 123 elongation factor for selenoprotein Ebola 124NM_021937.1 translation NP_068756.1 Transcription factor SMIF(HSA275986) Ebola 125-137 KIAA1026 Ebola 138 trinucleotide repeatcontaining 5 (TNRC5) Ebola 139 homogentisate 1,2-dioxygenase (HGD) Ebola140 region of chromosome Xq23-24 Ebola 141 region of chromosome 4p15.3Ebola 142 similar to LWamide neuropeptide Ebola 143 precursor protein[Hydractinia echinata] LOC129883 region of chromosome 2q21 Ebola 144region of chromosome Xp11.4, including Ebola 145 UPS9X LOC221829 Ebola146 U3 small nuclear RNA Ebola 147-154 integrin, beta 1 (ITGB1) Ebola155-158 BC020057; AAH20057.1 acrosornal vesicle protein 1 (ACRV1) andEbola 159 CHK1 checkpoint homolog (CHEK1) prospero-related homeobox 1(PROX1) Ebola 160 FLJ20627 and FLJ12910 Ebola 161-173 PIN2-interactingprotein (PINX1) and SRY Ebola 174 (sex-determining region Y)-box 7(SOX7) LOC131920 Ebola 175 region of chromosome 13q14 Ebola 176neurotropliic tyrosine kinase, receptor, type Ebola 177 3 (NTRK3) TERAprotein and FLJ13224 Ebola 178-179 LOC284260 Ebola 180 POM (POM121homolog) and ZP3 fusion Ebola 181-182 (POMZP3) DEAD/H box polypeptide 8(DDX8) and Ebola 183 similar to ribosomal protein L29 (cell) surfaceheparin binding protein HIP) (LOC284064) LOC345307 and UDP-N-acctyl-D-Ebola 184-186 galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GALNT7) Mus musculus 5S rRNApseudogene Ebola 187 (Rn5s-ps1) ribosomal protein L27a pseudogene Ebola188-192 (RPL27AP) and v-myb myeloblastosis viral oncogene homolog-like 2(MYBL2) Down's syndrome cell adhesion molecule Ebola 193 LOC148529 Ebola194 Huntingtin-associated protein interacting Ebola 195 NM_005338.4;protein (HAPIP) NP_005329.3 LOC158525 and similar to RIKEN cDNA Ebola196-200 1210001E11 (LOC347366) hypothetical protein FLJ12910 Ebola201-204 LOC350411 Ebola 205 allograft inflammatory factor 1 (AIF1) andEbola 206 HLA-B associated transcript 2 (BAT2) C10orf7 Ebola 207LOC346658 and LOC340349 Ebola 208-209 region of chromosome 12q21 Ebola210 LOC339248 and FLJ22659 Ebola 211 SR rich protein DKFZp564B0769 andEbola 212 hypothetical protein MGC14793 FLJ10439 Ebola 213-214NM_018093.1, NP_060563.1 cytochrome P450, family 11, subfamily A, Ebola215-218 polypeptide 1 (CYP11A1) and sema domain, immunoglobulin domain(Ig) and GPI membrane anchor, (semaphoring) 7A ribosomal protein S16(RPS 16) Ebola 219-220 BC004324.2; AAH04324.1 hypothetical proteinDKFZp434H0115 and Ebola 221-222 ATP citrate lyase (ACLY) calnexin(CANX); protein tyrosine Ebola 223-224 phosphatase, receptor type, K(PTPRK) cyclin M2 (CNNM2) Ebola 225 NM_017649.2; NP_060119.2 AXLreceptor tyrosine kinase (AXL) Ebola 226 BC032229; AAH32229.1 Homosapiens chromosome 10 open Ebola 227-228 reading frame 3 Homo sapienschromosome 10 open Ebola 229-230 reading frame 3 (C10orf3) Homo sapiensfer-1-like 3, myoferlin (C. Ebola 231-232 NM_013451.; elegans)NP_038479.1

Some of the host nucleic acids described in Table 1 and target sequencesassociated with SEQ ID NOS: 1-227, 229, and 231 encode polypeptides thatare receptors or ligands recognized by a particular virus, such as HIV,influenza A, or the Ebola virus. For example, the T-cell receptor V betaand V-D-J beta 2.1 chain polypeptides are part of the T-cell receptorcomplex that are recognized by certain glycoproteins in the HIVenvelope. Other host nucleic acids encode polypeptides that provide anenzymatic function related to a viral life cycle, such as the signalingpathways controlling viral packaging or enzymes involved in viralreplications. For example, the β-chimerin rho-GTPase may mediate acellular signal that initiates or triggers a process leading to passageof an HIV viral particle into the host cell. The data presented hereinindicate that Rab9 is involved in pathogen infectivity, for example byinterfering with trafficking of proteins and lipids within cells. Inparticular examples, it is demonstrated that Rab9 is involved in lipidraft formation, and that decreasing functional Rab9 and lipid raftsdecreases the ability of pathogens, such as viruses and bacteria, thathijack lipid rafts to bud or be infectious.

Still other host nucleic acids participate in the life cycle of a virus.For example, a certain nucleotide sequence of a host nucleic acid, suchas a gene within the host genome can be recognized during insertion andintegration of a viral genome (reverse transcribed into DNA from theviral RNA genomic template) into the host genome. Viral integration isdescribed in, for example, Coffin et al., Retroviruses, Chapter 5.

The nucleic acids and proteins disclosed herein can be identified,isolated, and characterized using any number of techniques of molecularbiology, including the specific methods and protocols described herein,such as in the examples below. In some examples, the nucleic acids wereidentified and isolated using the Lexicon Genetics, Inc. (The Woodlands,Tex.) “gene trap” technology disclosed in U.S. Pat. Nos. 6,080,576;6,136,566; 6,207,371; 6,139,833; 6,218,123 and 6,448,000.

Gene trap technology is a powerful method for cloning and identifyingfunctional genes, as it marks a gene with a tag and simultaneouslygenerates a corresponding genetic variation for that particular locus.The method involves introducing into a cell a DNA construct that canmonitor and potentially disrupt the transcriptional activity of theregion of the cell's genome into which it is inserted. The gene-trapmethod used to identify the host sequences is disclosed in U.S. Pat. No.6,448,000 (herein incorporated by reference).

Briefly, the gene trap protocol involves infecting a host cell (forexample, a cell of a Sup T-1 cell line (human), MDCK cells (canine), orVero cells (monkey)) with a recombinant vector (for example, U3neoSV1,FIG. 1). The recombinant vector includes a selectable maker or othersequence capable of being used to select infected host cells. However,the selectable marker or other sequence does not have a promoter at its5′ end. An exemplary selectable marker is a nucleic acid encodingresistance to an antibiotic (such as neomycin). A summary of the genetrap method is provided in FIGS. 2 and 3. Infection of the host cell isperformed in culture under conditions that yield about one copy of thevector per cell. The vector incorporates into the host cell genomeadjacent to an active promoter and interrupts or disrupts thetranscription of a nucleic acid in the host cell (FIG. 2). The hostpromoter drives expression of the selectable marker or other sequence onthe vector, and infected cells can then be selected. For example, if thevector carries a nucleic acid encoding neomycin resistance, cells can beselected on a medium that contains neomycin or G418, the neomycin analogfor mammalian cells, depending on the type of host cell used.

The selected host cells are expanded in culture to form a library ofcells that contain randomly disrupted host genes (FIG. 3). An aliquot ofthe library of cells is exposed to the appropriate virus, such as HIV,influenza A, or Ebola, to determine the effect of the disrupted hostsequence on viral infection of the host cells. Host cells that survivethe viral infection, or are relatively resistant to such infection (suchas those cells that survive for a longer period of time than about atleast 50% of the infected cells), can include one or more disruptedgenes involved in viral infection. Thus, by using the vector one candecrease viral or pathogenic infection of a host cell or in a subject.Therefore, by identifying these disrupted genes that decreased orotherwise interfered with viral infection of the host cell, candidatesequences are identified that can be used as targets to decrease orinhibit viral infection.

Those host cells that survive viral infection, or are relativelyresistant to such infection, are cloned, for example, by limit dilutionusing a chambered plate or by growth on methylcellulose. The interruptedhost nucleic acid is identified using standard molecular biologymethods. For example, host DNA can be isolated from the cell anddigested using an appropriate restriction enzyme to free the 5′ and 3′sequences adjacent the incorporated vector. The isolated DNA fragmentcan then be amplified, for example using PCR or by introducing the DNAfragment into a bacterial host cell then growing the bacteria. Onceisolated, the host nucleic acid can be further characterized andanalyzed. For example, the nucleic acid can be sequenced and compared toother similar nucleic acids. Methods of using these nucleic acids, andthe proteins encoded thereby, are discussed below.

Using these gene trap methods, several host molecules were identifiedthat were previously not known to be involved in viral pathogenesis (SEQID NOS: 1-232, Table 1, and target sequences associated with SEQ ID NOS:1-232). For example, the AMT gene (target sequences associated with SEQID NOS: 36 and 37) participates in influenza A infection of host cells.Fragments of host sequences involved in viral infection and pathogenesiscan now be identified, even including fragments or sequences that werepreviously known to be important in the pathogenesis of intracellularpathogens. For example, although the T-cell receptor was previouslyimplicated in HIV infection, the results disclosed herein demonstratethat the T-cell receptor V-D-J beta 2.1 chain (target sequencesassociated with SEQ ID NO: 20) is involved and in some examples requiredfor HIV infection, and host cells lacking the T-cell receptor V-D-J beta2.1 chain are unexpectedly highly resistant to HIV infection. Hence theV-D-J beta 2.1 chain is a target for anti-viral therapy at the DNA orpolypeptide level, and other pathogenically active subcomponents ofother known pathogenic sequences can also be identified with thismethod.

Examples of these host nucleic acid molecules are target sequencesassociated with SEQ ID NOS: 1-227, 229, and 231 (including variants,fragments, and fusions thereof) and summarized in Table 1. In additionto these specifically disclosed nucleotide sequences, a host nucleicacid can include nucleotide sequences that are similar to any of thetarget sequences associated with SEQ ID NOS: 1-227, 229, and 231, suchas having at least 70% identity, at least 80% identity, at least 85%identity, at least 90% identity, at least 95% identity, at least 98%identity, or even at least 99% identity to any of the target sequencesassociated with SEQ ID NOS: 1-227, 229, and 231. The disclosed hostnucleic acid sequences, and methods of using them, may comprise,consist, or consist essentially of any of the disclosed nucleic acidsequences shown in SEQ ID NOS: 1-227, 229, and 231, as well as targetsequences associated with SEQ ID NOS: 1-227, 229, and 231, or variantsor fragments thereof, or sequences that hybridize to the identifiedsequences under stringent or moderately stringent conditions.

The host nucleic acid molecules also include a fragment of any targetsequence associated with SEQ ID NOS: 1-227, 229, and 231, such as aprobe or primer as described below.

Host polypeptides corresponding to these nucleic acids also can be usedto practice the disclosed methods. In some examples, the polypeptideincludes an amino acid sequence that corresponds to a coding sequence ofany target sequence associated with SEQ ID NOS: 1-227, 229, and 231, ora target protein sequence associated with SEQ ID NOS: 228, 230, and 232.However, host polypeptides can also include those having similar aminoacid sequences, such as polypeptides that are at least 70% identical, atleast 80% identical, at least 90% identical, at least 95% identical, atleast 98% identical, or at least 99% identical to the amino acidsequences corresponding to translations of the coding sequence of anytarget sequence associated with SEQ ID NOS: 1-227, 229, and 231, or atarget protein sequence associated with SEQ ID NOS: 228, 230, and 232.For example, the disclosed host polypeptides and methods of using them,may comprise, consist, or consist essentially of an amino acid sequencecorresponding to a translation of the nucleotide sequence in any targetsequence associated with SEQ ID NOS: 1-227, 229, and 231, a targetprotein sequence associated with SEQ ID NOS: 228, 230, and 232, or anyof the protein sequences listed in Table 1. Alternatively, thepolypeptides include homologous polypeptides from other mammals (forexample human, monkeys, and dogs).

The host polypeptide can have an amino acid sequence that varies by oneor more conservative substitutions from the amino acid sequences of theproteins encoded by target sequences associated with SEQ ID NOS: 1-227,229, and 231, or from the target amino acid sequences associated withSEQ ID NOS: 228, 230, and 232. In one example, there is no more than 1,2, 3, 4, 5, or 10 conservative amino acid substitutions. In anotherexample, there are 1, 2, 3, 4, 5 or 10 conservative amino acidsubstitutions. The effects of these amino acid substitutions, deletions,or additions on host polypeptides can be assayed, for example, byanalyzing the ability of cells transformed with the derivative proteinsto resist infection by the corresponding virus.

Also included are fragments of any host polypeptide encoded by any ofthe target sequences associated with SEQ ID NOS: 1-227, 229, and 231, aswell as fragments of the target amino acid sequences associated with SEQID NOS: 228, 230, and 232. For example, a protein can include at least5-500 contiguous amino acids of the protein, such as at least 6-200, atleast 6100, at least 10-100, at least 10-50, or at least 20-50contiguous amino acids of the protein. A host polypeptide fragment canbe at least 5, at least 10, at least 15, at least 25, at least 50, atleast 100, at least 200, at least 500, or more amino acids of apolypeptide having an amino acid sequence corresponding to a codingregion of the nucleotide sequence in any of the target sequencesassociated with SEQ ID NOS: 1-227, 229, and 231, or a conservativevariant thereof, as well as target amino acid sequences associated withSEQ ID NOS: 228, 230, and 232.

Fragments of a nucleic acid target sequences associated with SEQ ID NOS:1-227, 229, and 231 can include 10-5000 contiguous nucleic acids, suchas 12-1000, 12-500, 15-100, or 18-50 contiguous nucleic acids. A hostnucleic acid fragment can be at least at least 5, at least 10, at least15, at least 20, at least 25, at least 50, at least 100, at least 200,at least 500, at least 1000, at least 2000, at least 5000 or morecontiguous nucleic acids in any target sequence associated with SEQ IDNOS: 1-227, 229, and 231, or a variant or fusion thereof.

Also included are host nucleic acids that encode the same polypeptideencoded by any target sequence associated with SEQ ID NOS: 1-227, 229,and 231, or a conservative variant of the polypeptide, or a fragmentthereof. For example, a host nucleic acid provided by target sequencesassociated with SEQ ID NOS: 36-37 encodes AMT. A second host nucleicacid also can encode an AMT having the same amino acid sequence as theAMT encoded by target sequences associated with SEQ ID NOS: 36-37, aconservative variant of this AMT, or a fragment thereof, yet this secondhost nucleic acid can have a different nucleotide sequence than a targetsequence associated with SEQ ID NOS: 36-37 due to the degeneracy of thegenetic code.

Methods of Using Host Sequences to Decrease Viral Infection

The interaction between a host nucleic acid or polypeptide (such astarget sequences associated with SEQ ID NOS: 1-232 and those shown inTable 1) and a virus or viral protein can be decreased or inhibitedusing the methods provided. Decreasing or inhibiting this interactioncan be used to decrease viral infection of a host cell, and/or todecrease symptoms associated with a viral infection in a subject. Forexample, decreasing or even inhibiting the interaction of a host nucleicacid or polypeptide and a virus can decrease, inhibit, or even preventinfection of a host cell by that virus, or otherwise inhibit theprogression or clinical manifestation of the viral infection. Inaddition, decreasing the interaction of a host nucleic acid orpolypeptide and a virus can reduce or alleviate one or more symptomsassociated with viral infection, such as a fever.

Several methods can be used to decrease or inhibit the interactionbetween a viral protein and a host protein or nucleic acid. The viraland host proteins or nucleic acids can be part of an in vitro solution,an in vivo expression system, or in situ with a host tissue or subject.The viral protein can be part of a larger molecule or complex, such asan envelope protein on the envelope of a mature virus or a fragment of aviral envelope. The host protein also can be part of a larger moleculeor complex, such as a host polypeptide expressed as part of a fusionprotein or contained as one subunit of a larger protein, such as atransport protein, cell receptor, structural protein, or an enzyme. Ahost nucleic acid can be part of a larger molecule, complex, organism ormicroorganism such as a host nucleic acid contained within its hostgenome, a recombinant vector, or a transgenic organism or microorganism(including both extrachromosomal molecules or genomic insertions).

In accordance with the disclosed methods, interaction is decreased orinhibited between a virus or viral protein and more than one (such as 2or more, such as 3 or more) host nucleic acids or polypeptides.Decreasing or inhibiting the interactions of one or more host nucleicacids or polypeptides with one or more viral proteins can have additiveor exponentially increasing effects. For example, it is believed thatdecreasing the interaction between a host T-ell receptor V-D-J beta 2.1chain and HIV, or decreasing the activity of a host β-chimerin, within ahost cell can enhance the inhibitory effect on HIV infection of thathost cell compared to inhibiting the interaction of only one of the hostpolypeptides. Hence, the methods include interfering with an interactionbetween the virus or viral protein and more than one of the proteinsassociated with infection by the same virus.

For example, for infection with HIV, the method could interfere withone, or two or more (such as three or more) of the following: T-cellreceptor V beta chain; T-ell receptor V-D-J beta 2.1 chain; β-chimerin(CHN2); malic enzyme 1; Hypothetical protein XP_(—)174419; sequence fromChromosome 4q31.3-32; alpha satellite DNA; LOC253788; LOC219938;coagulation factor III (F3); LOC91759; similar to KOX4 (LOC131880);LOC166140; LOC222474; similar to Rho guanine nucleotide exchange factor4, isoform a; APC-stimulated nucleotide exchange factor (LOC221178);T-cell receptor beta; ribosomal protein L7A-like 4 (RPL7AL4); v-srcsarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) (SRC);KIAA0564; alpha satellite DNA; M96 protein; hypothetical protein similarto G proteins (such as RAP-2A; LOC57826); LOC161005 and osteoblastspecific factor 2 (fasciclin I-like).

For Ebola virus, examples of targets include one, or two or more (suchas three or more) of the following: exportin 5; DNA polymerase eta(POLH); heterogenous nuclear riboprotein C (C1/C2); alpha-endosulfinepseudogene; LOC128741; LOC222888; LOC138421; zinc finger protein 297B;sideroflexin 5; importin 9; T-cell receptor beta; similar to murineputative transcription factor ZNF131 (LOC135952); KIAA1259; MURR1; CCT4;FLJ40773 and similar to ribosomal protein L24-like (LOC149360); testin2; testin 3; polybromo 1; DNA damage inducible transcript 3 (DDIT3);KIAA1887; PDZ and LIM domain 1 (elfin) (PDLIM1); LOC284803; PRO0097 andFLJ31958; small inducible cytokine E, member 1 (endothelialmonocyte-activating); E3 ubiquitin ligase (SMURF2) and MGC40489; Rab9;PRO1617 and retinoblastoma binding protein 1 (RBBP1); region ofchromosome 2q12; elongation factor for selenoprotein translation;transcription factor SMIF (HSA275986); KIAA1026; trinucleotide repeatcontaining 5; homogentisate 1,2 dioxygenase; region of chromosomeXq23-24; region of chromosome 4p15.3; similar to LWamide neuropeptideprecursor protein [Hydractinia echinata] (LOC129883); region ofchromosome 2q21; region of chromosome Xp11.4, including UPS9X;LOC221829; U3 small nuclear RNA; integrin, beta 1; acrosomal vesicleprotein 1 (ACRV1) and CHK1 checkpoint homolog (CHEK1); prospero-relatedhomeobox 1 (PROX1); FLJ20627 and FLJ12910; PIN2-interacting protein(PINX1) and SRY (sex-determining region Y)-box 7 (SOX7); LOC131920;region of chromosome 13q14; neurotrophic tyrosine kinase, receptor, type3 (NTRK3); TERA protein; FLJ13224; LOC284260; POM (POM121 homolog) andZP3 fusion (POMZP3); DEAD/H box polypeptide 8 (DDX8) and similar toribosomal protein L29 (cell surface heparin binding protein HIP)(LOC284064); LOC345307 and UDP-N-acetyl-D-galactosamine:polypeptideN-acetylgalactosaminyltransferase 7 (GALNT7); 5S rRNA pseudogene;ribosomal protein L27a pseudogene (RPL27AP) and v-myb myeloblastosisviral oncogene homolog-like 2 (MYBL2); Down's syndrome cell adhesionmolecule like 1; LOC148529; Huntingtin-associated protein interactingprotein; LOC158525 and similar to RIKEN cDNA 1210001E11 (LOC347366);hypothetical protein FLJ12910; LOC350411; allograft inflammatory factor1 (AIF1); HLA-B associated transcript 2 (BAT2); C10orf7; LOC346658;LOC340349; region of chromosome 12q21; LOC339248; FLJ22659; SR richprotein DKFZp564B0769; hypothetical protein MGC14793; FLJ10439;cytochrome P450, family 11, subfamily A, polypeptide 1; sema domain,immunoglobulin domain (Ig) and GPI membrane anchor, (semaphoring) 7A;ribosomal protein S16; hypothetical protein DKFZp434H0115; ATP citratelyase; calnexin; protein tyrosine phosphatase, receptor type, K (PTPRK);cyclin M2; AXL receptor tyrosine kinase; Homo sapiens chromosome 10 openreading frame 3, mRNA (cDNA clone MGC:3422 IMAGE:3028566); Homo sapienschromosome 10 open reading frame 3 (C10orf3); and Homo sapiensfer-1-like 3, myoferlin (C elegans) (FER1L3), transcript variant 1.

For influenza, examples of targets include one, or two or more (such asthree or more) of the following: T-cell leukemiatranslocation-associated (TCTA) gene, aminomethyltransferase;dystroglycan; BSN; LIM domain containing preferred translocation partnerin lipoma (LPP); sequence between LOC253121 and hyaluronan synthase 2(HAS2); testin 2; testin 3; PTPN1 gene for protein tyrosine phosphatase,non-receptor type 1; sequence between LOC149360 and LOC253961; sequencebetween KIAA1560 and tectorin beta; cadherin related 23;myeloid/lymphoma or mixed lineage leukemia, translocated to 10; malicenzyme 1; hypothetical protein XP-174419; and sequence from chromosome4q31.3-32.

In examples where a host polypeptide is a cell receptor or part of acell receptor, decreasing or preventing expression of the polypeptide,or altering the three-dimensional structure of the polypeptide, canreduce or inhibit the interaction between the host cell receptor and aviral protein. Similarly, decreasing, inhibiting or preventingexpression of a host ligand polypeptide (or altering the structure ofsuch a ligand) can decrease or inhibit an interaction between the viralprotein and the ligand. For example, decreasing or inhibiting expressionof one or more enzymes involved in viral pathogenesis, such as thoselisted in Table 1 and those target sequences associated with SEQ ID NOS:1-232, can block a component of the viral life cycle, such as blocking asignal pathway leading to transcription or translation of the viralgenome, or assembly of viral sub-parts. Decreasing or inhibiting theenzymatic activity of an enzyme (rather than its expression) can have asimilar effect

Altering the nucleotide sequence of a host nucleic acid, for example bytargeting disruption of the nucleotide sequence using complementarynucleic acid sequences, can decrease, inhibit or prevent integration ofa viral nucleic acid into the host nucleic acid. Methods that can beused to interrupt or alter translation of a host nucleic acid include,but are not limited to, using an antisense RNA, RNAi molecule, or ansiRNA that binds to a messenger RNA transcribed by the nucleic acidencoding a host polypeptide as described herein Decreasing or inhibitingthe expression of the host nucleic acid can also alter the course of thedisease. In one example, altering the nucleotide sequence of a host genethat is targeted by a virus for viral integration can decrease, inhibit,or even prevent, integration of that virus into the host genome.

A host nucleic acid involved in viral infection, including variants,fusions and fragments thereof, can be used to design agents that bind toa target sequence of that nucleic acid, such as antisense nucleic acidsor siRNAs. Such nucleic acid binding agents can be used to decrease orinhibit expression of the nucleic acid, to reduce the incidence of viralinfection. For example, an expression vector that transcribes antisenseRNA or siRNA that recognizes human β-chimerin mRNA is used to transformcell lines obtained from simians. These transformed cell lines areanalyzed for infection by simian immunodeficiency virus (SIV), which isrelated to HIV. If those cells are resistant to SIV infection, thedisrupted gene is identified, sequenced, and compared to the humanβ-chimerin gene. Sequence similarities between the two genes will offerinsight into common molecular mechanisms for infection by HIV and SIV,for example, common structural regions within their respectivetranslated proteins.

A binding agent that recognizes a host nucleic acid involved in viralinfection can be used for prophylactic or therapeutic purposes. Forexample, expression vectors having antisense RNA, RNAi molecules, orsiRNA molecules that target a host nucleic acid involved in viralinfection, such as β-chimerin, are introduced into the bone marrow of asubject. Uptake of the vector and expression of the antisense RNA, RNAi,or siRNA within cells infected by HIV offers a prophylactic ortherapeutic effect by disrupting the β-chimerin genes within thosecells, thus decreasing or inhibiting HIV infection. Similarly,expression vectors including Rab9 antisense RNA, RNAi, or siRNAmolecules can be introduced into the bone marrow of a subject. Uptake ofthe vector and expression of Rab9 antisense RNA, RNAi, or siRNA withincells infected by a pathogen that can hijack a lipid raft, such as HIVor Ebola, offers a prophylactic or therapeutic effect by disrupting theRab9 genes within those cells, thus decreasing or even inhibitinginfection by a pathogen that can hijack a lipid raft. The vector, orother nucleic acid carrying the nucleic acid specific binding agent, isintroduced into a subject by any standard molecular biology method andcan be included in a composition containing a pharmaceuticallyacceptable carrier.

Decreasing or inhibiting the interaction between a viral protein and ahost protein can decrease or inhibit viral infection. Methods that canbe used to decrease an interaction between a viral protein and one ormore host proteins (such as at least 2 host proteins, or at least 3 hostproteins), include but are not limited to, disrupting expression of ahost nucleic acid sequence encoding the host protein, (for example byfunctionally deleting the coding sequence, such as by a mutation,insertion, or deletion), altering the amino acid sequence or overallshape of the host protein, degrading the host protein, employing anagent that interferes with the viral protein or host protein (such as aspecific binding agent, for example an antibody or small molecule), or acombination thereof.

For example, expression of a host protein can occur during transcriptionor translation of a nucleic acid encoding the host protein, or as aresult of post-translational modification of a host protein. Methodsthat can be used to interrupt or alter transcription of a nucleic acidinclude, but are not limited to, site-directed mutagenesis, includingmutations caused by a transposon or an insertional vector; and providinga DNA-binding protein that binds to the coding region of the hostprotein, thus blocking or interfering with RNA polymerase or anotherprotein involved in transcription. Various inactive and recombinantDNA-binding proteins, and their effects on transcription, are discussedin Lewin, Genes VII. Methods that can be used to interrupt or altertranslation of a nucleic acid include, but are not limited to, using anantisense RNA or an siRNA that binds to a messenger RNA transcribed bythe nucleic acid encoding the host polypeptide as described herein.

For example, exemplary host T-cell receptor polypeptides are encoded bytarget sequences associated with SEQ ID NOS: 1-20. Disrupting theexpression of a nucleic acid including any target sequence associatedwith SEQ ID NOS: 1-20 can reduce or prevent production of thecorresponding T-cell receptor polypeptide, and without access to theT-cell receptor polypeptide, an HIV virus cannot infect the host cell.Even if expression of the host nucleic acid is not completely blocked ordisrupted, virus infection can still be inhibited. For example,interference with a host protein encoded by any target sequenceassociated with SEQ ID NOS: 1-20 reduces the number of T-cell receptorswithin that host cell available for recognition by an HIV virus, thusinhibiting HIV infection.

It is shown herein that inhibiting the interaction or activity betweenhost Rab9 and HIV and Ebola using Rab9 siRNA molecules decreasesinfection of a host cell by the virus compared to the amount ofinfection in the absence of the siRNA molecules.

Host proteins involved in viral infection, such as those encoded bytarget cDNA sequences associated with SEQ ID NOS: 1-227, 229, and 231,as well as target sequences associated with SEQ ID NOS: 228, 230, and232, can be used to generate specific binding agents to those proteins.The specific binding agent can be an anti-protein binding agent, such asa monoclonal or polyclonal antibody. Anti-protein binding agents canprovide a prophylactic or therapeutic effect, for example by interferingwith viral infection. Assays to determine whether an antibody interfereswith viral infection are described herein. Antibodies that recognize ahost protein involved in viral infection can prevent a virus or portionthereof (such as a viral protein) from binding to a host proteininvolved in viral infection. For example, a monoclonal or polyclonalantibody that binds to a V beta T-cell receptor on a cell can block thebinding of HIV to that T-cell receptor, thus blocking infection of thatcell. Effective amounts of such specific binding agents can beadministered alone to a subject, or as part of a pharmaceuticalcomposition, for the treatment of viral infection or as a prophylacticmeasure prior to the time the subject is exposed to the virus. Inanother example, specific binding agents that recognize a host proteininvolved in viral infection, such as β-chimerin or Rab9, can be used canbe used to screen for the presence of the host protein, in other cells,tissues or lysates, including a biological sample obtained from asubject.

Host nucleic acids and polypeptides described herein, such as targetsequences associated with SEQ ID NOS: 1-232, can be used forprophylactic or therapeutic uses. For example, polypeptides withstructures mimicking a protein recognized by a virus can be administeredto a subject as a pharmaceutical composition. These polypeptidesinteract with a virus already infecting that subject, or provide aprophylactic defense mechanism against infection if the subject is atrisk of exposure to a virus. For example, polypeptides structurallysimilar to the T-cell receptor V beta 2.1 chain are recognized by HIV.If such polypeptides are administered to an HIV-positive subject, theviruses already present in the subject interact with those polypeptidesin addition to that subject's T-cell receptors, thus inhibiting the rateat which my infects T-cells. The administered polypeptides act as“decoys” to block HIV from interacting with T-cell receptors. As anotherexample, an agent that otherwise interferes with the interaction betweena virus and a host protein can provide a similar prophylactic effect.For example, a chemical compound or anti-AMT binding agent (such as anantibody) that interferes with the interaction between AMT and aninfluenza virus (including an enzymatic inhibitor of AMT) provides aprophylactic or therapeutic effect against influenza A infection whenprovided to a host cell or administered to a host subject.

Additionally, the proteins described herein can be used to screensamples for the presence or absence of a particular antibody. Forexample, a β-chimerin or Rab9 protein can be used in an ELISA to screena sample obtained from an individual for the presence of anti-β-chimerinor anti-Rab9 antibodies generated by that individual, such as a bloodsample.

Using a method similar to that described for nucleic acid binding agentsabove, protein binding agents (such as agents that specifically bindβ-chimerin, Rab9, or V beta T-cell receptor proteins) can be used toscreen cells, individuals or populations for the presence or absence ofpolypeptides related to infection (such as HIV, Ebola, or influenzainfection), thus providing information about the susceptibility orresistance of that individual or population to viral infection.

The host nucleic acids, proteins, and related specific binding agentsdescribed herein can be used as models for the design of anti-viraldrugs. For example, the three-dimensional structure of a proteindescribed herein, such as β-chimerin, can be used in computer modelingof chemotherapeutic agents that block the activity of that moiety, forexample by binding the protein. As another example, a monoclonalantibody can be used in a competitive binding assay to screen for othercompounds that bind the same antigen.

Screening for Resistance to Infection

Also provided herein are methods of screening host subjects forresistance to infection by characterizing a nucleotide sequence of ahost nucleic acid or the amino acid sequence of a host polypeptide (suchas those shown in Table 1, or any target sequence associated with SEQ IDNOS: 1-232).

For example, the T-cell receptor V beta 2.1 chain nucleic acid of asubject can be isolated, sequenced, and compared to SEQ ID NO: 20 (or atarget sequence associated with SEQ ID NO: 20). The greater thesimilarity between that subject's V beta 2.1 chain nucleic acid and thesequence shown in SEQ ID NO: 20 (or a target sequence associated withSEQ ID NO: 20), the more susceptible that person is to HIV infection,while a decrease in similarity between that subject's V beta 2.1 chainnucleic acid and SEQ ID NO: 20 (or a target sequence associated with SEQID NO: 20), the more resistant that subject can be to HIV infection.

In another example, the aminomethyltransferase (AMT) nucleic acid of asubject can be isolated, sequenced, and compared to SEQ ID NOS: 36-37(or a target sequence associated with SEQ ID NOS: 36-37). The greaterthe similarity between that subject's AMT nucleic acid and the sequenceshown in SEQ ID NOS: 36-37 (or a target sequence associated with SEQ IDNOS: 36-37), the more susceptible that person is to influenza Ainfection, while a decrease in similarity between that subject's AMTnucleic acid and SEQ ID NOS: 36-37 (or a target sequence associated withSEQ ID NOS: 36-37), the more resistant that subject can be to influenzaA infection.

In yet another example, the Ras oncogene family member Rab9 nucleic acidof a subject can be isolated, sequenced, and compared to SEQ ID NOS:118-119 (or a target sequence associated with SEQ ID NOS: 118-119). Thegreater the similarity between that subject's Rab9 nucleic acid and thesequence shown in SEQ ID NOS: 118-119 (or a target sequence associatedwith SEQ ID NOS: 118-119), the more susceptible that person is toinfection by a pathogen that uses lipid rafts, such as those listed inTable 2, while a decrease in similarity between that subject's Rab9nucleic acid and SEQ ID NOS: 118-119 (or a target sequence associatedwith SEQ ID NOS: 118-119), the more resistant that subject nay be toinfection by a pathogen that uses lipid rafts.

Assessing the genetic characteristics of a population can provideinformation about the susceptibility or resistance of that population toviral infection. For example, polymorphic analysis of AMT alleles in aparticular human population, such as the population of a particular cityor geographic area, can indicate how susceptible that population is toinfluenza A infection. A higher percentage of AMT alleles substantiallysimilar to SEQ ID NOS: 36-37 (or a target sequence associated with SEQID NOS: 36-37) indicates that the population is more susceptible toinfluenza A infection, while a large number of polymorphic alleles thatare substantially different than SEQ ID NOS: 36-37 (or a target sequenceassociated with SEQ ID NOS: 36-37) indicates that a population is moreresistant to influenza A infection. Such information can be used, forexample, in making public health decisions about vaccinating susceptiblepopulations.

Transgenic Cells and Non-Human Mammals

Transgenic animal models, including recombinant and knock-out animals,can be generated from the host nucleic acids described herein. Exemplarytransgenic non-human mammals include, but are not limited to, mice,rats, chickens, cows, and pigs. In certain examples, a transgenicnon-human mammal has a knock-out of one or more of the target sequencesassociated with SEQ ID NOS: 1-35, and has a decreased viralsusceptibility, for example infection by HIV. In certain embodiments, atransgenic non-human mammal has a knock-out of any of the targetsequences associated with SEQ ID NOS: 36-63, and has a decreased viralsusceptibility, for example infection by influenza A. In certainexamples, a transgenic non-human mammal has a knock-out of any of thetarget sequences associated with SEQ ID NOS: 64-232, and has a decreasedviral susceptibility, for example infection by Ebola. In certainexamples, a transgenic non-human mammal has a knock-out of any targetsequence associated with SEQ ID NOS: 118-119, and has a decreasedsusceptibility to infection by a pathogen that uses a lipid raft, suchas those listed in Table 2. Such knock-out animals are useful forreducing the transmission of viruses from animals to humans. Inaddition, animal viruses that utilize the same targets provided hereincan be decreased in the animals.

Expression of the sequence used to knock-out or functionally delete thedesired gene can be regulated by chosing the appropriate promotersequence. For example, constitutive promoters can be used to ensure thatthe functionally deleted gene is never expressed by the animal. Incontrast, an inducible promoter can be used to control when thetransgenic animal does or does not express the gene of interest.Exemplary inducible promoters include tissue-specific promoters andpromoters responsive or unresponsive to a particular stimulus (such aslight, oxygen, chemical concentration, such as a tetracycline induciblepromoter).

For example, a transgenic mouse including an AMT gene (such as a targetsequence associated with SEQ ID NOS: 36-37), or a mouse having adisrupted AMT gene, can be examined during exposure to various mammalianviruses related to influenza A. Comparison data can provide insight intothe life cycles of influenza and related viruses. Moreover, knock-outanimals (such as pigs) that are otherwise susceptible to an infection(for example influenza) can be made to determine the resistance toinfection conferred by disruption of the gene.

Transgenic pigs having a disrupted human protein tyrosine phosphatasegene can be produced and used as an animal model to determine othertypes of infections, including viral infections in mammals related toinfluenza A. A transgenic pig resistant to infection by viruses otherthan influenza A is used to demonstrate the relatedness of influenza andthose other viruses. Transgenic animals, including methods of making andusing transgenic animals, are described in various patents andpublication, such as WO 01/43540; WO 02/19811; U.S. Pub. Nos:2001-0044937 and 2002-0066117; and U.S. Pat. Nos. 5,859,308; 6,281,408;and 6,376,743; and the references cited therein.

Cells including an altered or disrupted host nucleic acid or polypeptidehaving a role in viral infection (such as a target sequence associatedwith SEQ ID NOS: 1-232), are resistant to infection by a virus (seeExample 2). Such cells may therefore include cells having decreasedsusceptibility to HIV infection (such as cells having altered ordisrupted target sequence associated with SEQ ID NOS: 1-35), Ebolainfection (such as cells having altered or disrupted target sequenceassociated with SEQ ID NOS: 64-232), or influenza A (such as cellshaving altered or disrupted target sequence associated with SEQ ID NOS:36-63). For example, cells in which a β-chimerin gene was died using thegene-trap method remain CD4⁺ after HIV infection and do not producefurther detectable HIV virus particles. Thus, disrupting the expressionof β-chimerin can confer resistance on the cell to infection by HIV.Additionally, interfering with the activity of β-chimerin, such ascontacting a β-chimerin with an enzymatic inhibitor or ananti-β-chimerin binding agent, can confer a similar resistance to HIVinfection.

Screening for Agents that Decrease Viral Infection

A host nucleic acid or polypeptide involved in viral infection, such asa target sequence associated with SEQ ID NOS: 1-232, and peptides listedin Table 1, can be used to identify agents that inhibit the binding of avirus or viral protein to a host nucleic acid, a host protein, oranother target protein capable of binding to the virus or viral protein.In some examples, a host molecule, such as a host protein or nucleicacid is contacted with a viral molecule, such as a virus or portionthereof, for example as a viral protein. One or more test agents arecontacted with the host molecule, the viral molecule, both bothmolecules, before, during or after contacting the host and viralmolecules. Subsequently, it is determined whether binding of the viralmolecule to the host molecule is decreased in the presence of the testagent, wherein a decrease in binding is an indication that the testagent decreases the binding of viral protein to the target protein.

In other examples, a cell-based assay is used to identify proteins thatdecrease viral infection, for example using the yeast two-hybrid system.

For example, the binding of the T-cell receptor V-D-J beta 2.1 chainpolypeptide to HIV (or an HIV envelope glycoprotein) can be determinedin the presence of a test agent. A decrease in binding activity betweenthe T-cell receptor V-D-J beta 2.1 chain polypeptide and HIV indicatesthat the test agent decreases the binding of HIV to the T-cell receptorV-D-J beta 2.1 chain, and the agent is a candidate for use as ananti-HIV agent. A decrease in binding activity can be determined by acomparison to a reference standard, such as a binding activity reportedin the scientific literature, or to a control. Any suitable compound orcomposition can be used as a test agent, such as organic or inorganicchemicals, including aromatics, fatty acids, and carbohydrates;peptides, including monoclonal antibodies, polyclonal antibodies, andother specific binding agents; or nucleic acids. The virus or viralmolecule can be obtained from any suitable virus, such as HIV, influenzaA, Ebola, and related viruses.

Therapeutic agents identified with the disclosed approaches can be usedas lead compounds to identify other agents having even greater antiviralactivity. For example, chemical analogs of identified chemical entities,or variant, fragments of fusions of peptide agents, are tested for theirability to decrease viral infection using the disclosed assays.Candidate agents are also tested tested for safety in animals and thenused for clinical trials in animals or humans.

Microarrays

The host nucleic acids or proteins disclosed herein having a role inviral infection, such as a target sequence associated with SEQ ID NOS:1-232, can be used in an array. The array can be a microarray, such as anucleic acid array that includes probes to different polymorphic allelesof a human AMT gene (for example target sequence associated with SEQ IDNOS: 36-37) or a human Rab9 gene (for example target sequence associatedwith SEQ ID NOS: 118-119). Kits can be generated, such as diagnostickits or kits for screening for the presence or absence of a host nucleicacid within a biological sample obtained from a subject or kits foradministering an effective amount of a specific binding agent to asubject for a therapeutic or prophylactic purpose.

The following examples are provided to illustrate particular features ofcertain embodiments, but the scope of the claims should not be limitedto those features exemplified.

EXAMPLE 1 Generation of Cells with Increased Resistance to ViralInfection

The gene-trap method was used to identify cellular genes needed forviral propagation but whose inactivation is not lethal to the host cell.This was accomplished by using a Moloney murine leukemia virus-derivedshuttle vector that encodes for a promoterless neomycin-resistance gene(FIG. 1). This vector integrates into the host genome attranscriptionally active genes, thereby disrupting the host gene bututilizing the host promoter to drive neomycin resistance carried by thevector. The cells are then infected with the desired virus. Cellssurviving the viral infection carry an interrupted host gene that isneeded during the viral life cycle. Since the construct is a shuttlevector, it can function as a plasmid and can be moved from mammalian tobacterial systems, facilitating subcloning and DNA sequencing. Usingthis approach, loci involved in, and in some cases required for viralinfection, for example by HIV-1 and HIV-2, influenza A and Ebola viruswere identified.

Tissue Culture

Sup-T1 human lymphoblastic leukemia cells were cultured in RPMI-1640medium supplemented with 10% heat-inactivated fetal calf serum (FCS),penicillin, streptomycin and Fungisome. MDCK normal canine kidney cellswere cultured in DMEM supplemented with 10% fetal bovine serum (FBS),penicillin, streptomycin. Vero African green monkey kidney cells werecultured in DMEM supplemented with 10% FBS, amphotericin B,streptomycin, and Glutamine. All cultures were grown under 5% CO₂.Selection by all media was done in the presence of either 1 mg/ml(Sup-T1 and MDCK cells) or 400 mg/ml G418 (Geneticin; Vero cells).

Generation of Gene-Trapped Library of Cells

Parental, virus sensitive cells were plated and infected with U3neoSV1as follows. Retrovirus vectors were obtained from H. Earl Ruley(Department of Microbiology and Immunology, Vanderbilt University Schoolof Medicine, Nashville, Tenn.). Stocks of the U3neoSV1 virus wereprepared as described (Chen et al., Gene trap retroviruses in Methods inMolecular Genetics (1994), page 123, herein incorporated by reference).

FIG. 1 illustrates the U3neoSV1 retroviral vector, which contains apromoterless neomycin phosphotransferase gene (Neo^(R)) within the U3unique sequence of the 5′ long terminal repeat (LTR) of MMLV.Additionally, a second mutationally inactivated copy of neo is presentin the 3′ LTR. Portions of the MMLV genome were removed to impairreplication, and were replaced with the β-lactamase gene which confersampicillin resistance (Amp^(R)) to E. coli as well as an E. coli originof replication (ori), flanked by two unique restriction sites for BamHI(position 2570) and EcoRI (position 4175). Sites and orientations ofprimers used for sequence analysis of cloned genomic fragments areindicated by the triangular arrowheads.

Parental, virus sensitive cells (106 Sup-T1 for HIV, Madin-Darby caninekidney, (MDCK) for influenza A, or Vero cells for Ebola) were plated for12 hours before infection, after which U3neoSV1 was added at amultiplicity of infection (MOI) of 0.1, as titered by adding 1 ml ofdiluted stocks to cultured cells in the presence of 4 μg/ml polybrene.The cells were incubated at 37° C. for one hour, 10 ml of fresh mediumadded, and the cells were incubated overnight at 37° C. The next day,the medium was replaced with the appropriate media containing 1 mg/mlG418 and maintained until surviving cells approached confluence, whichwas usually about two weeks.

Upon random integration of the U3neoSV1 vector into the host genome,endogenous promoters result in expression of Neo^(R), while expressionof the exons 3′ to the site of integration is disrupted. Therefore, onlythose events occurring at transcriptionally active promoters ofnon-essential genes are selected.

A pool of the surviving cells, termed a library, including many cellsbearing different disrupted genes was then exposed to the pathogen ofinterest. The resulting Sup-T1 library cells, MDCK library cells, andVero library cells were infected HIV-1 and HIV-2; the A/PR/8/34 virusreassortant having A/Johannesburg/82/96 glycoproteins (H1N1); and Ebola,respectively, as follows.

An aliquot of the cell library was infected with three rounds of HIV-1and three rounds of HIV-2 (3Bx in BC7 cells), normally a lethal eventfor Sup T-1 cells (FIG. 4). Approximately 3×10⁸ actively growing Sup-T1library cells were infected with the CXCR4 cytopathic HIV-1 strain LAIat an MOI of 10, approximately 100 fold greater that that normally usedfor spreading infection in culture. The cells were incubated with thevirus for four hours in 2 ml of medium, then grown in bulk at 10⁶cells/ml for two weeks, at which time G418 was added to a finalconcentration of 1 mg/ml and the cultures continued for an additionaltwo weeks. The surviving cells were exposed to two further rounds ofHIV-1 infection as described above and shown in FIG. 4.

Following HIV-1 infection, surviving cells were incubated 1:100 with BC7T cells constitutively expressing the HIV-2 strain 3BX, which wasmodified to infect regardless of CD4 status, solely using the CXCR4receptor. Cells were coincubated for two weeks followed by selectionwith 1 mg/ml G418 (same as FIG. 4, but with HIV-2 instead of HIV-1). Thesurviving cells were exposed to two further rounds of HIV-2 infection.

The final cell culture was selected using anti-CD4 magnetic microbeads(Miltyni) and divided into 2.0 ml cultures containing 1000 cells eachThese were then infected with LAI at an MOI of 10. Surviving cells fromeach culture were subjected to limit dilution, or growth onmethylcellulose, and expanded in selection medium. The isolated cloneswere identified as being CD4 and CXCR4 positive following flow cytometryanalysis using standard protocols. Several cell isolates were resistantto further HIV infection with unique expression of CD4 cell surfaceantigen.

For influenza infection, approximately 10⁷ actively growing MDCK librarycells were washed with phosphate buffered saline (Gibco) and infectedwith the A/PR/8/34 virus reassortant having A/Johannesburg/82/96glycoproteins (H1N1) at an MOI of 20-30 in 250 μl DMEM in a T-25 flask.The cells were incubated with the virus for two hours, and the inoculumwas subsequently replaced with DMEM, supplemented with 2% FBS and 1μg/ml TPCK trypsin (to cleavage-activate HA of new progeny virus). Thecells were incubated for 18 hours to provide 2-3 rounds of infection.The maintenance medium was removed and replaced with selection medium(DMEM with 10% FBS and 1 mg/ml neomycin) and survivors allowed toexpand. The surviving cells were exposed to one additional round ofinfection as described.

For filovirus infection, vero library cells were infected with eitherthe Gulu 2000 or Zaire 1976 Ebola (EBO) strains, or the Voege 1967strain of Marburg (MBG) at an MOI of greater than one in T-75 flasks inmedium supplemented with 400 mg/ml G418. After a cytopathic effect (CPE)of 4+ was attained (greater than one week), survivors were harvested andreseeded undiluted and at 1:16 and 1:256 dilutions in selection mediumWells with growth after 10 or more days were reinoculated into T12.5flasks in selection medium and allowed to expand.

Cells surviving Ebola or influenza infection were cloned by eitherlimiting dilution or growth on methylcellulose. The isolates werecharacterized phenotypically by flow cytometry and the interrupted genedetermined by inverse PCR, cloning into BAC, or by the use of theshuttle feature of the vector followed by DNA sequence analysis.

EXAMPLE 2 Cloning and Sequencing of Trapped Genes

This example describes the methods used to clone the sequencesconferring resistance to the library of cells surviving viral infection.The identified sequences (SEQ ID NOS: 1-227, 229, 231) encode hostproteins that are involved in pathogen infection, and in some cases arerequired for the infectivity by the pathogen.

Isolation of Trapped Genes

The genomic DNA from actively growing virus-resistant isolates wasextracted, prepared, and electroporated into cells as follows. CellularDNA from actively growing virus-resistant isolates was extracted fromone million cells using the QIAmp DNA Blood Mini Kit (Qiagen, Inc.)according to the manufacturer's instructions. Genomic DNA was digestedat a final concentration of 150 μg/ml with either EcoRI or BamHI (NewEngland Biolabs) at 1.5 or 2 units/μl, respectively (see FIG. 1).Digested DNA was ethanol precipitated using oyster glycogen (Sigma) as acarrier, resuspended to a final concentration of 60 ng/μl and ligatedusing T4 DNA ligase (New England Biolabs). Genomic digestion resulted inthe fragmentation of the retrovirus and the genomic DNA. Ligations weresubsequently ethanol precipitated in the presence of glycogen,resuspended in 3 μl water and used directly to transform E. coli.

A 1.5 μl aliquot of each precipitated ligation was added to thawedGenehog cells (Invitrogen) or SURE cells (Stratagene), electroporatedusing a GenePulser (BioRad) according to the manufacturer'sinstructions, and plated onto Luria broth (LB) agar (1% tryptone, 0.5%yeast extract, 0.5% NaCl, 2% agar) containing 100 μg/μl carbenicillin(Sigma). Clones were isolated after 24 hours and used to inoculate 3 mlLB containing 100 μg/μl carbenicillin. Plasmid DNA was prepared afterovernight growth using the QIAprep Spin Miniprep Kit (QIAGEN, Inc.)according to the manufacturer's instructions and eluted in water.

Sequencing of Shuttle Clones

Due to the position of the unique sites in U3neoSV1, BamHI digestionfacilitates cloning of DNA 3′ to the site of integration, while EcoRIdigestion results in the cloning of genomic DNA 5′ to the site ofintegration. Using oligonucleotides homologous to the U3neoSV1 fragment,the sequence of the disrupted genomic DNA flanking the gene-trapinsertion site was determined as follows.

Sequencing reactions were performed using the ABI BigDye terminatorcycle sequencing kit with reaction products resolved on either an ABI3100 Genetic Analyzer or an ABI 377 DNA Sequencer (Applied Biosystems,Foster City, Calif.). Sequences were obtained by using oligonucleotides5′-ATCTTGTCAATCATGCG (SEQ ID NO: 235) and 5′-GGGTCIGACGCrCATG (SEQ IDNO: 236) for EcoRI-generated shuttle clones, or 5′-GATAGGTGCCTCACRG (SEQID NO: 237) for BamHI-generated shuttle clones.

Sequence Analysis

Sequences obtained from shuttle clones were analyzed by the RepeatmaskerWeb Server, available on the Internet at the website for the Departmentof Molecular Biotechnology, University of Washington, followed bystandard nucleotide-nucleotide BLAST (blastn) against the NationalCenter for Biotechnology Information database, including nr(non-redundant GenBank+EMBL+DDBJ+PDB sequences), est (expressed sequencetags) and htgs (unfinished High Throughput Genomic Sequences: phases 0,1 and 2). Additionally, a nucleotide-protein database (blastx) analysiswas performed against the nr database.

Candidate Host Genes Required for Pathogenesis

Candidate host genes required for the indicated pathogen, which werecloned via the gene-trap method and sequenced, are presented in Table 1and in SEQ ID NOS: 1-226. The CD4⁺, latently infected, noninfectiousHIV-resistant isolates 18B, 18E, 2B, and 2E were used to recover thegenes involved in HIV-1 and HIV-2 pathogenesis, influenza A-resistantisolates B1, B3, B5, B6, and B7 were use to recover the host genesinvolved in influenza A pathogenesis, and Ebola-resistant isolates ZVand MV were used to recover the host genes involved in Ebolapathogenesis. Candidate genes can be validated by siRNA and cDNAcomplementation, as described in Example 3.

In summary, using the U3neoSV1 gene-trap, sixteen HIV-1 and -2 resistantSup-T1 cell lines, and fifteen influenza A resistant MDCK cell lineswere isolated and characterized. Twenty-three EBO-Zaire resistant Verocell line pools, twenty-four EBO-Gulu resistant pools, and thirty MBGresistant pools were screened. The shuttle-vector design of the U3neoSV1gene-trap allowed identification of multiple host genes involved in thepathogenesis of HIV-1, HIV-2, influenza A, and Ebola, which aredescribed herein and summarized in Table 1 and sequences provided in SEQID NOS: 1-232. Cross-resistance of resistant isolates to multiplepathogens can be quickly examined to reveal common pathways in the virallife cycles.

EXAMPLE 3 siRNA Molecules Decrease Viral Infection

This example describes methods used to express siRNAs that recognizeRab9 (such as a target sequence associated with SEQ ID NOS: 118-119),AXL (AXL receptor tyrosine kinase; such as a target sequence associatedwith SEQ ID NO: 226), CHN (beta-chimerin; such as a target sequenceassociated with SEQ ID NOS: 21-22), KOX (such as a target sequenceassociated with SEQ ID NO: 30), RBB (retinoblastoma binding protein 1;such as a target sequence associated with SEQ ID NOS: 120-122),KIAA1259; F3 (such as a target sequence associated with SEQ ID NO: 29),and Mselb (mammalian selenium binding protein; such as a target sequenceassociated with SEQ ID NO: 124).

The following Rab9 siRNA sequences were generated by Dharmacon, RNATechnologies (Lafayette, Colo.) using chemical synthesis:GGGAAGAGTTCACITATGA (SEQ ID NO: 238); TCACAAAGCTTCCAGAACT (SEQ ID NO:239); GTAACAAGATTGACATAAG (SEQ ED NO: 240); and GGAAGTGGATGGACATTTT (SEQD NO: 241).

The following AXL (AXL receptor tyrosine kinase) siRNA sequences weregenerated by Dharmacon, RNA Technologies using chemical synthesis:GGUCAGAGCUGGAGGAUUU (SEQ ID NO: 242); GAAAGAAGGAGACCCGLTUA (SEQ ID NO:243); CCAAGAAGAUCUACAAUGG (SEQ ID NO: 244); and GGAACUGCAUGCUGAAUGA (SEQID NO: 245).

siRNA sequences were also used that recognized CHN (beta-chimerin); KOX(similar to KOX4 (LOC131880) and LOC166140); RBB (retinoblastoma bindingprotein 1); KIAA1259; F3 and mammalian selenium binding protein. Oneskilled in the art will understand that siRNA sequences that recognizeother sequences involved in viral infection (such as a target sequenceassociated with any of SEQ ID NOS: 1-232) can be desiged and prepared bycommercial entities, such as Dharmacon, RNA Technologies.

The four siRNA sequences for each gene (CHN, KOX, RBB, RAB, KIAA1259,F3, ASL and Mselb) were separately pooled. Each of the eight pools ofsiRNAs, hybridized to its appropriate complement sequence, were used totransfect JC53 (HeLa cells modified to accept HIV), Vero (monkey kidneycells), MDCK (dog kidney cells), or HEK (human kidney cells). All cellswere obtained from American Type Culture Collection (ATCC, Mannassas,Va.). GFP siRNA sequences were used as a negative control.

Cells (20,000 to 250,000) were incubated in serum free media for 24hours. Cocktails were made by mixing the appropriate duplex siRNAs(50-100 pmoles) with lipofectamine 2000 (4-16 μl) and RNAse Inhibitor(1-4 μl) in a solution of Optimem (serum free medium) in a total volumeof 200-2000 μl. The lipofectamine was allowed to incubate at roomtemperature for 5 minutes before the addition of siRNA. Aliquots (50-500μl) of the cocktail were added to the cells which were incubated at 37°C. for 48 hours. The cells were then infected with HIV, Ebola, orinfluenza and the incubation continued for 3-7 days. Followingtransfection, several assays were conducted to confirm transfectionefficiency, and to determine the resistance of the cells to infection byvarious agents.

Quantitation of p24 levels in HIV infected JC53 cells was determinedusing the Coulter HIV-1 p24 Antigen Neutralization Kit according to themanufacturers recommendation. As shown in FIG. 5, Rab9 siRNAs andmammalian selenium binding protein siRNAs each decreased HIV infectionby about 50% on day 4 post infection (day 7 post addition of siRNA). Inaddition, HIV infection decreased by about 80-90% in the presence ofbeta-chimerin siRNAs, KOX (similar to KOX4 (LOC131880) and LOC166140)siRNAs, or retinoblastoma binding protein 1 siRNAs. However, HIVinfection did not decrease in the presence of siRNAs that recognizeKIAA1259, tissue factor 3, or AXL receptor tyrosine kinase. It ispossible that apoptosis is interrupted by the siRNAs, so the cell livesthrough the infection but still makes virus. It is also possible thatthe p24 levels are elevated but is not associated with infectiousparticles.

To determine the level of Ebola infection in HEK293 cells transfectedwith Rab9 or AXL siRNA, the presence of gp1 antigen was determined byusing a fluorescent antibody to gp1 envelope protein. Infection by Eboladecreased by at least about 90-95% in the presence of Rab9 siRNA, ascompared to the amount of infection in the absence of Rab9 siRNA.Infection by Ebola decreased by at least about 80% in the presence ofAXL siRNA, as compared to the amount of infection in the absence of AXLsiRNA.

EXAMPLE 4 Expression of Rab9 siRNA Decreases Lipid Raft Formation

As described in Example 3, siRNA molecules that recognize Rab9 decreaseviral infection Rab9 transports late endosomes to trans-golgi. Based onthese results, a model is proposed whereby Rab9 plays a role in lipidraft formation (FIG. 6). Lipid rafts are liquid-ordered microdomainsenriched in sphingolipds and cholesterol and are involved inbiosynthetic traffic, signal transduction, and endocytosis. Viruses takeadvantage of (“hijack”) rafts for completion of some steps of theirreplication cycle, such as entry into their cell host, assembly, andbudding. Without wishing to be bound to a particular theory, it isproposed that Rab9 trafficks cholesterol, the dynamic glue that holdslipid rafts together. Further evidence for this hypothesis is based onobservations of Neimann-Pick type C disease cells. Neimann-Pick type Cis a genetic disease that results in accumulation of abnormally highlevels of intracellular cholesterol. However, over expression of Rab9 inNeimann-Pick type C disease cells, decreases the level of cholesterol.

Examples of pathogens that hijack lipid rafts include, but are notlimited to those shown in Table 2. In the absence of functional Rab9 andlipid rafts (or a decrease in the number of rafts), viruses may not beable to bud or be infectious. Therefore, the use of agents that decreaseor inhibit Rab9 expression or activity can be used to decrease infectionby other pathogens, as well as toxins such as anthrax, that hijack lipidrafts, such as those shown in Table 2. TABLE 2 Pathogens that hijacklipid rafts. Bacteria Intracellular Toxin survivalbinding/oligomerization Viruses Protozoa Campylobaceer Vibrio choleraeSV40 Toxoplasma gondii jujuni Legionella Aeromonas hydrophilia EchovirusI and II Plasmodium pneumophila falciparum Brucella spp Clostridium spp.Avian sarcoma and leukosis virus FimH and Dr Streptcoccus pyogenesSemiliki forest virus Escherichia coli Salmonella Bacillus anthracisEcotropic mouse typhimurium leukaemia virus Shigella flexneri Bacillusthuringiensis HTLV-I Chlamydia spp. Heliobacter pylori HIV-1Mycobacterium Lysteria monocytogenes Ebola and Marburg spp. virusesMeasles virus Herpes Simplex virus Influenza virus Epstein-Barr virus

This example therefore illustrates that identification of an agent (suchas a small molecule or siRNA) that inhibits a particular pathogen can beused to inhibit other pathogens that have a similar mechanism of action.

EXAMPLE 5 RNAi Molecules

This example describes methods that can be used to decease or inhibitexpression of any of the genes listed in Table 1, or target sequencesassociated with SEQ ID NOS: 1-232, to decrease viral infection, such asinfection by HIV, Ebola, or influenza. Exemplary RNAi compounds areprovided for several different genes, such as beta-chimerin receptortyrosine kinase, retinoblastoma binding protein 1, Homo sapienschromosome 10 open reading frame 3, Homo sapiens fer-1-like 3, myoferlin(C. elegans), transcript variant 1, Homo sapiens chromosome 10 openreading frame 3 (C10orf3), malic enzyme, cadherin related 23,sideroflexin 5, polybromo 1, elongation factor for selenoproteintranslation, integrin, beta 1, huntingtin interacting protein 1 andcyclin M2.

One skilled in the art will understand that RNAi molecules can begenerated to any of the genes listed in Table 1. Although only 27mersare shown in SEQ ID NOS: 246-845, this disclosure is not limited to RNAicompounds of a particular length. An RNAi molecule can be any length,such as at least about about 25 nucleotides, or even as many as 400nucleotides. One skilled in the art will also understand that RNAisequences that recognize other sequences involved in viral infection(such as a target sequence associated with any of SEQ ID NOS: 1-232) canbe desiged and prepared by commercial entities, such as Sequitur, Inc.(Natick, Mass.).

Using the methods described in Example 3, the disclosed RNAi compoundsare used to decrease viral infection. For example, a 27mer RNAi compoundshown in any of SEQ ID NOS: 246-845 is incubated with its reversecomplement, allowing hybridization of the two molecules. In particularexamples, two or more, such as three or more, 27mer RNAi compounds aretransfected into a cell. This duplex molecule is contacted with a cell,such as a cell of a subject in whom decreased viral infection isdesired, under conditions that allow the duplex to enter the cell.

EXAMPLE 6 Disruption of Gene Expression

This example describes methods that can be used to disrupt expression ofa host gene, such as those shown in Table 1 and target sequencesassociated with SEQ ID NOS: 1-232, and thereby decrease activity of theproteins encoded by these sequences. Such methods are useful when it isdesired to decrease or inhibit viral infection. In a particular example,disrupted expression of at least one target sequence associated with SEQID NOS: 1-232 in a host cell is used to treat a subject having a viralinfection, or susceptible to a viral infection. Methods useful fordisrupting gene function or expression are the use of antisenseoligonucleotides, siRNA molecules (see Example 3), RNAi molecules (seeExample 5), ribozymes, and triple helix molecules. Techniques for theproduction and use of such molecules are well known to those of skill inthe art.

Antisense Methods

To design antisense oligonucleotides, a host mRNA sequence is examined.Regions of the sequence containing multiple repeats, such as TTTTTTTT,are not as desirable because they will lack specificity. Severaldifferent regions can be chosen. Of those, oligos are selected by thefollowing characteristics: those having the best conformation insolution; those optimized for hybridization characteristics; and thosehaving less potential to form secondary structures. Antisense moleculeshaving a propensity to generate secondary structures are less desirable.

Plasmids including antisense sequences that recognize one or more of thetarget sequences associated with SEQ ID NOS: 1-232 (such as a sequencethat encodes a protein listed in Table 1) can be generated usingstandard methods. For example, cDNA fragments or variants coding for ahost protein involved in viral infection are PCR amplified. Thenucleotides are amplified using Pfu DNA polymerase (Stratagene) andcloned in antisense orientation a vector, such as pcDNA vectors (InVitrogen, Carlsbad, Calif.). The nucleotide sequence and orientation ofthe insert can be confirmed by sequencing using a Sequenase kit(Amersham Pharmacia Biotech).

Generally, the term “antisense” refers to a nucleic acid capable ofhybridizing to a portion of a host RNA sequence (such as mRNA) by virtueof some sequence complementarity. The antisense nucleic acids disclosedherein can be oligonucleotides that are double-stranded orsingle-stranded, RNA or DNA or a modification or derivative thereof,which can be directly administered to a cell, or which can be producedintracellularly by transcription of exogenous, introduced sequences.

Antisense nucleic acids are polynucleotides, and can be oligonucleotides(ranging from about 6 to about 100 oligonucleotides). In one example, anantisense polynucleotide recognizes one or more of the target nucleicacid sequences associated with SEQ ID NOS: 1-227, 229, or 231. Inspecific examples, the oligonucleotide is at least 10, 15, or 100nucleotides, or a polynucleotide of at least 200 nucleotides. However,antisense nucleic acids can be much longer. The nucleotide can bemodified at the base moiety, sugar moiety, or phosphate backbone, andcan include other appending groups such as peptides, or agentsfacilitating transport across the cell membrane (Letsinger et al., Proc.Natl. Acad. Sci. USA 1989, 86:6553-6; Lemaitre et al., Proc. Natl. Acad.Sci. USA 1987, 84:648-52; WO 88/09810) or blood-brain barrier (WO89/10134), hybridization triggered cleavage agents (Krol et al.,BioTechniques 1988, 6:958-76) or intercalating agents (Zon, Pharm. Res.3:539-49, 1988).

An antisense polynucleotide (including oligonucleotides) that recognizesone or more of the target sequences associated with SEQ ID NOS: 1-227,229, or 231, can be modified at any position on its structure withsubstituents generally known in the arL For example, a modified basemoiety can be 5-fluorouracil, 5-bromouracil, 5-chlorouracil,5-iodouracil, hypoxanthine, xanthine, acetylcytosine,5-(carboxyhydroxylmethyl) uracil,5-carboxymethylaminomethyl-2-thiouridine,5-carboxymethylaminomethyluracil, dihydrouracil,beta-D-galactosylqueosine, inosine, N-6-sopentenyladenine,1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine,2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine,7-methylguanine, 5-methylaminomethyluracil,methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarboxymethyluracil, 5-methoxyuracil,2-methylthio-N-6-isopentenyladenine, uracil-5-oxyacetic acid,pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil,2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acidmethylesters uracil-5-oxyacetic acid, 5-methyl-2-thiouracil,3-(3-amino-3-N-2-carboxypropyl) uracil, and 2,6-diaminopurine.

An antisense polynucleotide that recognizes one or more of the targetsequences associated with SEQ ID NOS: 1-227, 229, or 231, can include atleast one modified sugar moiety such as arabinose, 2-fluoroarabinose,xylose, and hexose, or a modified component of the phosphate backbone,such as phosphorothioate, a phosphorodithioate, a phosphoramidothioate,a phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkylphosphotriester, or a formacetal or analog thereof.

In a particular example, an antisense polynucleotide that recognizes oneor more of the target sequences associated with SEQ ID NOS: 1-227, 229,or 231 is an α-anomeric oligonucleotide. An α-anomeric oligonucleotideforms specific double-stranded hybrids with complementary RNA in which,contrary to the usual β-units, the strands run parallel to each other(Gautier et al., Nucl. Acids Res. 15:6625-41, 1987). The oligonucleotidecan be conjugated to another molecule, such as a peptide, hybridizationtriggered cross-linking agent, transport agent, orhybridization-triggered cleavage agent. Oligonucleotides can include atargeting moiety that enhances uptake of the molecule by host cells. Thetargeting moiety can be a specific binding molecule, such as an antibodyor fragment thereof that recognizes a molecule present on the surface ofthe host cell.

Polynucleotides disclosed herein can be synthesized by standard methods,for example by use of an automated DNA synthesizer. As examples,phosphorothioate oligos can be synthesized by the method of Stein et al.(Nucl. Acids Res. 1998, 16:3209), methylphosphonate oligos can beprepared by use of controlled pore glass polymer supports (Sarin et al.,Proc. Natl. Acad. Sci. USA 85:7448-51, 1988). In a specific example,antisense oligonucleotide that recognizes one or more of the targetsequences associated with SEQ ID NOS: 1-227, 229, or 231 includescatalytic RNA, or a ribozyme (see WO 90/11364, Sarver et al., Science247:1222-5, 1990). In another example, the oligonucleotide is a2′-0-methylribonucleotide (Inoue et al., Nucl. Acids Res. 15:6131-48,1987), or a chimeric RNA-DNA analogue (Inoue et al., FEBS Lett.215:327-30, 1987).

The antisense polynucleic acids disclosed herein include a sequencecomplementary to at least a portion of an RNA transcript of a gene, suchas a target sequence associated with SEQ ID NOS: 1-227, 229, or 231.However, absolute complementarity, although advantageous, is notrequired. A sequence can be complementary to at least a portion of anRNA, meaning a sequence having sufficient complementarily to be able tohybridize with the RNA, forming a stable duplex; in the case ofdouble-stranded antisense nucleic acids, a single strand of the duplexDNA may thus be tested, or triplex formation can be assayed. The abilityto hybridize depends on the degree of complementarity and the length ofthe antisense nucleic acid. Generally, the longer the hybridizingnucleic acid, the more base mismatches with an RNA it may contain andstill form a stable duplex (or triplex, as the case may be). One skilledin the art can ascertain a tolerable degree of mismatch by use ofstandard procedures to determine the melting point of the hybridizedcomplex.

The relative ability of polynucleotides (such as oligonucleotides) tobind to complementary strands is compared by determining the T_(m), of ahybridization complex of the poly/oligonucleotide and its complementarystrand. The higher the T_(m) the greater the strength of the binding ofthe hybridized strands. As close to optimal fidelity of base pang aspossible achieves optimal hybridization of a poly/oligonucleotide to itstarget RNA.

The amount of antisense nucleic acid that is effective in the treatmentof a particular disease or condition (the therapeutically effectiveamount) depends on the nature of the disease or condition, and can bedetermined by standard clinical techniques. For example, it can beuseful to use compositions to achieve sustained release of an antisensenucleic acid, for example an antisense molecule that recognizes one ormore target sequences associated with SEQ ID NOS: 1-227, 229, or 231. Inanother example, it may be desirable to utilize liposomes targeted viaantibodies to specific cells.

As an alternative to antisense inhibitors, catalytic nucleic acidcompounds, such as ribozymes or anti-sense conjugates, can be used toinhibit gene expression. Ribozymes can be synthesized and administeredto the subject, or can be encoded on an expression vector, from whichthe ribozyme is synthesized in the targeted cell (as in WO 9523225, andBeigelman et al. Nucl. Acids Res. 1995, 23:4434-42). Examples ofoligonucleotides with catalytic activity am described in WO 9506764.Conjugates of antisense with a metal complex, such as terpyridylCu (II),capable of mediating mRNA hydrolysis, are described in Basklin et al.(Appl. Biochem Biotechnol. 54:43-56, 1995).

Ribozymes

Ribozymes are enzymatic RNA molecules capable of catalyzing the specificcleavage of RNA. The mechanism of ribozyme action involves sequencespecific hybridization of the ribozyme molecule to complementary targetRNA, followed by a endonucleolytic cleavage. Methods of using ribozymesto decrease or inhibit RNA expression are known in the art. An overviewof ribozymes and methods of their use is provided in Kashani-Sabet (J.Imvestig. Dermatol. Symp. Proc., 7:76-78, 2002).

Ribozyme molecules include one or more sequences complementary to thetarget host mRNA and include the well-known catalytic sequenceresponsible for mRNA cleavage (see U.S. Pat. No. 5,093,246, hereinincorporated by reference).

A ribozyme gene directed against any of the target sequences associatedwith SEQ ID NOS: 1-227, 229, or 231 can be delivered to a subjectendogenously (where the ribozyme coding gene is transcribedintracellularly) or exogenously (where the ribozymes are introduced intoa cell, for example by transfection). Methods describing endogenous andexogenous delivery are provided in Marschall et al. (Cell Mol.Neurobiol. 14:523-38, 1994).

Specific ribozyme cleavage sites within any potential RNA target areinitially identified by scanning the target molecule for ribozymecleavage sites that include the following sequence: GUA, correspondingto the region of the target gene containing the cleavage site may beevaluated for predicted structural features, such as secondarystructure, that may render the oligonucleotide sequence unsuitable. Thesuitability of candidate targets may also be evaluated by testing theiraccessibility to hybridization with complementary oligonucleotides,using ribonuclease protection assays.

For example, a plasmid that contains a ribozyme gene directed against aβ-chimerin rho-GTPase, placed behind a promoter, can be transfected intothe cells of a subject, for example a subject susceptible to HIVinfection. Expression of this plasmid in a cell will decrease or inhibitβ-chimerin rho-GTPase RNA expression in the cell. In another example, aplasmid that contains a riboyzme gene directed against Rab9 placedbehind a promoter, can be transfected into the cells of a subject, forexample a subject susceptible to infection by a pathogen that utilizeslipid rafts, such as Ebola. Expression of this plasmid in a cell willdecrease or inhibit Rab9 RNA expression in the cell. Other examples ofusing ribozymes to decrease or inhibit RNA expression can be found in WO01/83754 (herein incorporated by reference).

Triple Helix Molecules

Nucleic acid molecules used in triplex helix formation should be singlestranded and composed of deoxynucleotides. The base composition of theseoligonucleotides is ideally designed to promote triple helix formationvia Hoogsteen base pairing rules, which generally require sizeablestretches of either purines or pyrimidines to be present on one strandof a duplex. Nucleotide sequences may be pyrimidine-based, which willresult in TAT and CGC+ triplets across the three associated strands ofthe resulting triple helix. The pyrimidine-rich molecules provide basecomplementarity to a purine-rich region of a single strand of the duplexin a parallel orientation to that strand. In addition, nucleic acidmolecules may be chosen that are purine-rich, for example, contain astretch of guanidine residues. These molecules will form a triple helixwith a DNA duplex that is rich in GC pairs, in which the majority of thepurine residues are located on a single strand of the targeted duplex,resulting in GGC triplets across the three strands in the triplex.

Alternatively, the potential sequences that can be targeted for triplehelix formation may be increased by creating a so called “switchback”nucleic acid molecule. Switchback molecules are synthesized in analternating 5′-3′,3′-5′ manner, such that they base pair with one strandof a duplex first and then the other, eliminating the necessity for asizeable stretch of either purines or pyrimidines to be present on onestrand of a duplex.

EXAMPLE 7 Methods of Treatment

When the activity of a host cell protein or nucleic acid involved inviral infection is decreased by prematurely downregulating their levelsof expressing using antisense molecules, a reduction in viral infectioncan be achieved. Antisense oligonucleotides, RNAi molecules, ribozymes,and siRNA molecules that recognize a host nucleic acid involved in viralinfection (Example 6) can therefore be used to disrupt cellularexpression of a host protein involved in viral infection. The disclosedantisense, ribozyme, RNAi molecules and siRNA molecules can beadministered to a subject alone, or in combination with othertherapeutic agents such as anti-viral compounds.

A subject susceptible to or suffering from a viral infection, whereindecreased amounts of infection by the virus is desired, can be treatedwith a therapeutically effective amount of antisense, ribozyme, RNAimolecule or siRNA molecule (or combinations thereof) that recognizes ahost sequence involved in viral infection, such as those shown in Table1 or target sequences associated with SEQ ID NOS: 1-232. After theantisense, ribozyme, RNAi molecule or siRNA molecule has produced aneffect (a decreased level of viral infection is observed, or symptomsassociated with viral infection decrease), for example after 24-48hours, the subject can be monitored for diseases associated with viralinfection.

Similarly, other agents, such as an antibody that recognizes a hostprotein involved in viral infection and prevents the protein frominteracting with a viral protein, can also be used to decrease orinhibit viral infection. Other exemplary agents are those identifiedusing the methods described in the Examples below. These agents, such asantibodies, peptides, nucleic acids, organic or inorganic compounds, canbe can be administered to a subject in a therapeutically effectiveamount. After the agent has produced an effect (a decreased level ofviral infection is observed, or symptoms associated with viral infectiondecrease), for example after 24-48 hours, the subject can be monitoredfor diseases associated with viral infection.

The treatments disclosed herein can also be used prophylactically, forexample to inhibit or prevent a viral infection. Such administration isindicated where the treatment is shown to have utility for treatment orprevention of the disorder. The prophylactic use is indicated inconditions known or suspected of progressing to disorders associatedwith a viral infection.

EXAMPLE 8 Recombinant Expression

With the disclosed host sequences involved in viral infection, nativeand variant sequences can be generated. Expression and purification bystandard laboratory techniques of any variant, such as a polymorphism,mutant, fragment or fusion of a sequence involved in viral infection,such as a target sequence associated with SEQ ID NOS: 1-232, is enabled.One skilled in the art will understand that the sequences involved inviral infection, as well as variants thereof, can be producedrecombinantly in any cell or organism of interest, and purified prior touse.

Methods for producing recombinant proteins are well known in the art.Therefore, the scope of this disclosure includes recombinant expressionof any host protein or variant or fragment thereof involved in viralinfection. For example, see U.S. Pat. No. 5,342,764 to Johnson et al.;U.S. Pat. No. 5,846,819 to Pausch et al.; U.S. Pat. No. 5,876,969 toFleer et al. and Sambrook et al. (Molecular Cloning: A LaboratoryManual, Cold Spring Harbor, N.Y., 1989, Ch. 17, herein incorporated byreference).

Briefly, partial, full-length, or variant cDNA sequences that encode fora protein involved in viral infection, such as a target sequenceassociated with SEQ ID NOS: 1-232, can be ligated into an expressionvector, such as a bacterial expression vector. Proteins or peptides canbe produced by placing a promoter upstream of the cDNA sequence.Examples of promoters include, but are not limited to lac, trp, tac,trc, major operator and promoter regions of phage lambda, the controlregion of fd coat protein, the early and late promoters of SV40,promoters derived from polyoma, adenovirus, retrovirus, baculovirus andsimian virus, the promoter for 3-phosphoglycerate kinase, the promotersof yeast acid phosphatase, the promoter of the yeast alpha-matingfactors and combinations thereof.

Vectors suitable for the production of intact proteins include pKC30(Shimatake and Rosenberg, 1981, Nature 292:128), pKK177-3 (Amann adBrosius, 1985, Gene 40:183) and pET-3 (Studiar and Moffatt, 1986, J.Mol. Biol. 189:113). A DNA sequence can be transferred to other cloningvehicles, such as other plasmids, bacteriophages, cosmids, animalviruses and yeast artificial chromosomes (YACs) (Burke et al., 1987,Science 236:806-12). These vectors can be introduced into a variety ofhosts including somatic cells, and simple or complex organisms, such asbacteria, fungi (Timberlake and Marshall, 1989, Science 244:1313-7),invertebrates, plants (Gasser and Fraley, 1989, Science 244:1293), andmammals (Pursel et al., 1989, Science 244:1281-8), that are renderedtransgenic by the introduction of the heterologous cDNA.

For expression in mammalian cells, a cDNA sequence, such as a codingsequence of any target sequence associated with SEQ ID NOS: 1-227, 229,or 231, can be ligated to heterologous promoters, such as the simianvirus SV40, promoter in the pSV2 vector (Mulligan and Berg, 1981, Proc.Natl. Acad. Sci. USA 78:2072-6), and introduced into cells, such asmonkey COS-1 cells (Gluzman, 1981, Cell 23:175-82), to achieve transientor long-term expression. The stable integration of the chimeric geneconstruct may be maintained in mammalian cells by biochemical selection,such as neomycin (Southern and Berg, 1982, J. Mol. Appl. Genet.1:327-41) and mycophoenolic acid (Mulligan and Berg, 1981, Proc. Natl.Acad. Sci. USA 78:2072-6).

The transfer of DNA into eukaryotic, such as human or other mammaliancells is a conventional technique. The vectors are introduced into therecipient cells as pure DNA (transfection) by, for example,precipitation with calcium phosphate (Graham and vander Eb, 1973,Virology 52:466) strontium phosphate (Brash et al., 1987, Mol. Cell Bol.7:2013), electroporation (Neumann et al., 1982, EMBO J. 1:841),lipofection (Felgner et al., 1987, Proc. Natl. Acad. Sci USA 84:7413),DEAE dcextran (McCuthan et al., 1968, J. Natl. Cancer Inst. 41:351),microinjection (Mueller et al., 1978, Cell 15:579), protoplast fusion(Schafner, 1980, Proc. Nattl. Acad. Sci. USA 77:2163-7), or pellet guns(Klein et al., 1987, Nature 327:70). Alternatively, the cDNA can beintroduced by infection with virus vectors, for example retroviruses(Bernstein et al., 1985, Gen. Engrg. 7:235) such as adenoviruses (Ahmadet al., J. Virol. 57:267, 1986) or Herpes (Spaete et al., Cell 30:295,1982).

EXAMPLE 9 Pharmaceutical Compositions and Modes of Administration

Various delivery systems for administering the therapies disclosedherein are known, and include encapsulation in liposomes,microparticles, microcapsules, expression by recombinant cells,receptor-mediated endocytosis (Wu and Wu, J. Biol. Chem. 1987,262:4429-32), and construction of therapeutic nucleic acids as part of aretroviral or other vector. Methods of introduction include, but are notlimited to, topical, intradermal, intramuscular, intraperitoneal,intravenous, subcutaneous, intranasal, and oral routes. The compoundscan be administered by any convenient route, for example by infusion orbolus injection, by absorption through epithelial or mucocutaneouslinings (for example, oral mucosa, rectal, vaginal and intestinalmucosa, etc.) and can be administered together with other biologicallyactive agents. Administration can be systemic or local. Pharmaceuticalcompositions can be delivered locally to the area in need of treatment,for example by topical application.

Pharmaceutical compositions are disclosed that include a therapeuticallyeffective amount of an RNA, DNA, antisense molecule, ribozyme, RNAimolecule, siRNA molecule, specific-binding agent, or other therapeuticagent, alone or with a pharmaceutically acceptable carrier. Furthermore,the pharmaceutical compositions or methods of treatment can beadministered in combination with (such as before, during, or following)other therapeutic treatments, such as other antiviral agents.

Delivery Systems

The pharmaceutically acceptable carriers useful herein are conventional:Remington's Pharmaceutical Sciences, by Martin, Mack Publishing Co.,Easton, Pa., 15th Edition (1975), describes compositions andformulations suitable for pharmaceutical delivery of the therapeuticagents herein disclosed. In general, the nature of the carrier willdepend on the mode of administration being employed. For instance,parenteral formulations usually include injectable fluids that includepharmaceutically and physiologically acceptable fluids such as water,physiological saline, balanced salt solutions, aqueous dextrose, sesameoil, glycerol, ethanol, combinations thereof, or the like, as a vehicle.The carrier and composition can be sterile, and the formulation suitsthe mode of administration. In addition to biologically-neutralcarriers, pharmaceutical compositions to be administered can containminor amounts of non-toxic auxiliary substances, such as wetting oremulsifying agents, preservatives, and pH buffering agents and the like,for example sodium acetate or sorbitan monolaurate.

The composition can be a liquid solution, suspension, emulsion, tablet,pill, capsule, sustained release formulation, or powder. For solidcompositions (for example powder, pill, tablet, or capsule forms),conventional non-toxic solid carriers can include, for example,pharmaceutical grades of mannitol, lactose, starch, sodium saccharine,cellulose, magnesium carbonate, or magnesium stearate. The compositioncan be formulated as a suppository, with traditional binders andcarriers such as triglycerides.

Embodiments of the disclosure including medicaments can be prepared withconventional pharmaceutically acceptable carriers, adjuvants andcounterions as would be known to those of skill in the art.

The amount of therapeutic agent effective in decreasing or inhibitingviral infection can depend on the nature of the virus and its associateddisorder or condition, and can be determined by stdard clinicaltechniques. In addition, in vitro assays can be employed to identifyoptimal dosage ranges. The precise dose to be employed in theformulation will also depend on the route of administration, and theseriousness of the disease or disorder, and should be decided accordingto the judgment of the practitioner and each subject's circumstances.Effective doses can be extrapolated from dose-response curves derivedfrom in Wtro or animal model test systems.

The disclosure also provides a pharmaceutical pack or kit comprising oneor more containers filled with one or more of the ingredients of thepharmaceutical compositions. Optionally associated with suchcontainer(s) can be a notice in the form prescribed by a governmentalagency regulating the manufacture, use or sale of pharmaceuticals orbiological products, which notice reflects approval by the agency ofmanufacture, use or sale for human administration. Instructions for useof the composition can also be included.

Adminlitration of Nucleic Acids

In an example in which a nucleic acid is employed to reduce viralinfection, such as an antisense, RNAi molecule, or siRNA molecule, thenucleic acid can be delivered intracellularly (for example by expressionfrom a nucleic acid vector or by receptor-mediated meclinisms), or by anappropriate nucleic acid expression vector which is administered so thatit becomes intracellular, for example by use of a retroviral vector (seeU.S. Pat. No. 4,980,286), or by direct injection, or by use ofmicroparticle bonmardment (such as a gene gun; Biolistic, Dupont), orcoating with lipids or cell-surface receptors or transfecting agents, orby administering it in linkage to a homeobox-like peptide which is knownto enter the nucleus (for example Joliot et al., Proc. Natl. Acad. Sci.USA 1991, 88:1864-8). The present disclosure includes all forms ofnucleic acid delivery, including synthetic oligos, naked DNA, plasmidand viol, integrated into the genome or not.

EXAMPLE 10 In Vitro Screening Assay for Agents that Decrease ViralInfection

This example describes in vitro methods that can be used to screen testagents for their ability to interfere with or even inhibit viralinfection of a host cell. As disclosed in the Examples above, thedisclosed host proteins (such as those listed in Table 1 and the targetprotein sequences associated with SEQ ID NOS: 1-232, as well asvariants, fragments, and fusions thereof) are involved in viralinfection (such as infection by HIV, Ebola, and influenza A), and thehost protein/viral protein interaction is a component in the ability ofa virus to infect a cell. Therefore, screening assays can be used toidentify and analyze agents that decrease or interfere with thisinteraction. For example, the following assays can be used to identifyagents that interfere with the interaction of the disclosed hostproteins (such as those listed in Table 1 and the target proteinsequences associated with SEQ ID NOS: 1-232) with a viral proteinsequence. However, the present disclosure is not limited to theparticular methods disclosed herein.

Agents identified via the disclosed assays can be useful, for example,in decreasing or even inhibiting viral infection by more than an amountof infection in the absence of the agent, such as a decrease of at leastabout 10%, at least about 20%, at least about 50%, or even at leastabout 90%. This decrease in viral infection can serve to amelioratesymptoms associated with viral infection, such as fever. Assays fortesting the effectiveness of the identified agents, are discussed below.

Exemplary test agents include, but are not limited to, any peptide ornon-peptide composition in a purified or non-purified form, such aspeptides made of D-and/or L-configuration amino acids (in, for example,the form of random peptide libraries; see Lam et al., Nature 354:824,1991), phosphopeptides (such as in the form of random or partiallydegenerate, directed phosphopeptide libraries; see, for example,Songyang et al., Cell 72:767-78, 1993), antibodies, and small or largeorganic or inorganic molecules. A test agent can also include a complexmixture or “cocktail” of molecules.

The basic principle of the assay systems used to identify agents thatinterfere with the interaction between a host protein, such as thoselisted in Table 1 and the target protein sequences associated with SEQID NOS: 1-232, and its viral protein binding partner or partners,involves preparing a reaction mixture containing the host protein and aviral protein under conditions and for a time sufficient to allow thetwo proteins to interact and bind, thus forming a complex. In order totest an agent for inhibitory activity, the reaction is conducted in thepresence and absence of the test agent. The test agent can be initiallyincluded in the reaction mixture, or added at a time subsequent to theaddition of a host protein and a viral protein. Controls are incubatedwithout the test agent or with a placebo. Exemplary controls includeagents known not to bind to viral or host proteins. The formation of anycomplexes between the host protein and the viral protein is thendetected. The formation of a complex in the control reaction, but not inthe reaction mixture containing the test agent, indicates that the agentinterferes with the interaction of the host protein and the viralprotein, and is therefore possibly an agent that can be used to decreaseviral infection.

The assay for agents that interfere with the interaction of host andviral proteins can be conducted in a heterogeneous or homogeneousformat. Heterogeneous assays involve anchoring the host protein or theviral protein onto a solid phase and detecting complexes anchored on thesolid phase at the end of the reaction. In some examples, the methodfurther involves quantitating the amount of complex formation orinhibition. Exemplary methods that can be used to detect the presence ofcomplexes, when one of the proteins is labeled, include ELISA,spectrophotometry, flow cytometry, and microscopy. In homogeneousassays, the entire reaction is performed in a liquid phase. In eithermethod, the order of addition of reactants can be varied to obtaindifferent information about the agents being tested. For example, testagents that interfere with the interaction between the proteins, such asby competition, can be identified by conducting the reaction in thepresence of the test agent, for example by adding the test agent to thereaction mixture prior to or simultaneously with the host protein andviral protein. On the other hand, test agents that disrupt preformedcomplexes, such as agents with higher binding constants that displaceone of the proteins from the complex, can be tested by adding the testagent to the reaction mixture after complexes have been formed. Thevarious formats are described briefly below.

Once identified, test agents found to inhibit or decrease theinteraction between a host protein and a viral protein can be formulatedin therapeutic products (or even prophylactic products) inpharmaceutically acceptable formulations, and used for specifictreatment or prevention of a viral disease, such as HIV, Ebola, orinfluenza A.

Heterogeneous Assay System

In a heterogeneous assay system, one binding partner, either the hostprotein (such as those listed in Table 1 and target protein sequencesassociated with SEQ ID NOS: 1-232) or the viral protein (such as an HIV,Ebola, or influenza A virus preparation) is anchored onto a solidsurface (such as a microtiter plate), and its binding partner, which isnot anchored, is labeled, either directly or indirectly. Exemplarylabels include, but are not limited to, enzymes, fluorophores, ligands,and radioactive isotopes. The anchored protein can be immobilized bynon-covalent or covalent attachments. Non-covalent attachment can beaccomplished simply by coating the solid surface with a solution of theprotein and drying. Alternatively, an immobilized antibody (such as amonoclonal antibody) specific for the protein can be used to anchor theprotein to the solid surface. The surfaces can be prepared in advanceand stored.

To conduct the assay, the binding partner of the immobilized species isadded to the coated surface with or without the test agent. After thereaction is complete, unreacted components are removed (such as bywashing) and any complexes formed will remain immobilized on the solidsurface. The detection of complexes anchored on the solid surface can beaccomplished in a number of ways. Where the binding partner waspre-labeled, the detection of label immobilized on the surface indicatesthat complexes were formed. Where the binding partner is notpre-labeled, an indirect label can be used to detect complexes anchoredon the surface; for example by using a labeled antibody specific for thebinding partner (the antibody, in turn, may be directly labeled orindirectly labeled with a labeled anti-Ig antibody). Depending upon theorder of addition of reaction components, test compounds which inhibitcomplex formation or which disrupt preformed complexes can be detected.

Alternatively, the reaction can be conducted in a liquid phase in thepresence or absence of the test agent, the reaction products separatedfrom unreacted components, and complexes detected; for example by usingan immobilized antibody specific for one binding partner to anchor anycomplexes formed in solution, and a labeled antibody specific for theother binding partner to detect anchored complexes. Again, dependingupon the order of addition of reactants to the liquid phase, test agentswhich inhibit complex or which disrupt preformed complexes can beidentified.

Homogenous Assays

In an alternate example, a homogeneous assay can be used. In thismethod, a preformed complex of the host protein and the viral protein isprepared in which one of the proteins is labeled, but the signalgenerated by the label is quenched due to complex formation (forexample, see U.S. Pat. No. 4,109,496 by Rubenstein which utilizes thisapproach for immunoassays). The addition of a test substance thatcompetes with and displaces one of the binding partners from thepreformed complex will result in the generation of a signal abovebackground. In this way, test agents that disrupt host protein-viralprotein interactions are identified.

Immobilization of Proteins

In a particular example, a host protein involved in viral infection(such as those listed in Table 1 and the target protein sequencesassociated with SEQ ID NOS: 1-232) can be prepared for immobilizationusing recombinant DNA techniques. For example, a coding region of aprotein listed in Table 1, or any target sequence associated with SEQ IDNOS: 1-232, can be fused to a glutathione. S-transferase (GST) geneusing the fusion vector pGEX-5X-1, in such a manner that its bindingactivity is maintained in the resulting fusion protein. The viralprotein (such as an Ebola, HIV, or influenza A protein or viralpreparation) can be purified and used to raise a monoclonal antibody,using methods routinely practiced in the art and described above. Thisantibody can be labeled with the radioactive isotope ¹²⁵I using methodsroutinely practiced in the art.

In a heterogeneous assay, for example, the GST-host fusion protein canbe anchored to glutathione-agarose beads. The viral protein preparationcan then be added in the presence or absence of the test agent in amanner that allows interaction and binding to occur. At the end of thereaction period, unbound material can be washed away, and the labeledmonoclonal antibody can be added to the system and allowed to bind tothe complexed binding partners. The interaction between the host proteinand the viral protein can be detected by measuring the amount ofradioactivity that remains associated with the glutathione-agarosebeads. A successful inhibition of the interaction by the test compoundwill result in a decrease in measured radioactivity.

Alternatively, the GST-host fusion protein and the viral protein can bemixed together in liquid in the absence of the solid glutathione agarosebeads. The test agent can be added either during or after the bindingpartners are allowed to interact. This mixture can then be added to theglutathione-agarose beads and unbound material is washed away. Again,the extent of inhibition of the binding partner interaction can bedetected by adding the labeled antibody and measuring the radioactivityassociated with the beads.

In another example, these same techniques can be employed using peptidefragments that correspond to the binding domains of the host protein andthe viral protein, respectively, in place of one or both of the fulllength proteins. Any number of methods routinely practiced in the artcan be used to identify and isolate the proteins binding site. Thesemethods include, but are not limited to, mutagenesis of one of the genesencoding the proteins and screening for disruption of binding in aco-immunoprecipitation assay. Compensating mutations in a host gene canbe selected. Sequence analysis of the genes encoding the respectiveproteins will reveal the mutations that correspond to the region of theprotein involved in interactive binding. Alternatively, one protein canbe anchored to a solid surface using methods described in above, andallowed to interact with and bind to its labeled binding partner, whichhas been treated with a proteolytic enzyme, such as trypsin. Afterwashing, a short, labeled peptide comprising the binding domain mayremain associated with the solid material, which can be isolated andidentified by amino acid sequencing. Also, once the gene coding for thefor the cellular or extracellular protein is obtained, short genesegments can be engineered to express peptide fragments of the protein,which can then be tested for binding activity and purified orsynthesized.

For example, a host protein can be anchored to a solid material asdescribed above by making a GST-host protein fusion protein and allowingit to bind to glutathione agarose beads. The viral protein can belabeled with a radioactive isotope, such as ³⁵S, and cleaved with aproteolytic enzyme such as trypsin. Cleavage products can then be addedto the anchored GST-host protein fusion protein and allowed to bind.After washing away unbound peptides, labeled bound material,representing the cellular or extracellular protein binding domain, canbe elute purified, and analyzed for amino acid sequence. Peptides soidentified can be produced synthetically or fused to appropriatefacilitative proteins using recombinant DNA technology.

EXAMPLE 11 Cell-Based Screening Assay for Agents that Decrease ViralInfection

This example describes methods using intact cells that can be used toscreen test agents for their ability to interfere with or even inhibitviral infection of a host cell. For example, a yeast two-hybrid assay orthe inverse two-hybrid assay method of Schreiber and coworkers (Proc.Natl. Acad. Sci., USA 94:13396, 1977) is used to screen for an agentthat disrupts the association between a host protein (such as thoselisted in Table 1, proteins encoded by any target sequence associatedwith SEQ ID NOS: 1-227, 229, and 231, and any target sequence associatedwith SEQ ID NOS: 229, 230, and 232) and a viral protein (such as HIV,Ebola, or influenza A virus). Similar to Example 10, therapeutic agentsidentified by these approaches are tested for their ability to decreaseor inhibit infection of a host cell, such as a human cell, by HIV,Ebola, or influenza A.

In one example, the yeast two-hybrid system is used to identifyanti-viral agents. One version of this system has been described (Chienet al., Proc. Natl. Acad. Sci. USA, 88:9578-82, 1991) and iscommercially available from Clontech (Palo Alto, Calif.). Briefly,utilizing such a system, plasmids are constructed that encode two hybridproteins: one includes the DNA-binding domain of a transcriptionactivator protein fused to one test protein “X” and the other includesthe activator proteins activation domain fused to another test proteinfly. Thus, either “X” or “Y” in this system can be a host protein (suchas those listed in Table 1 and any target sequences associated with SEQID NOS: 1-232), while the other can be a test protein or peptide. Theplasmids are transformed into a strain of Saccharomyces cerevisiae thatcontains a reporter gene (such as lacZ) whose regulatory region containsthe activators binding sites. Either hybrid protein alone cannotactivate transcription of the reporter gene, the DNA-binding domainhybrid because it does not provide activation function and theactivation domain hybrid because it cannot localize to the activator'sbinding sites. Interaction of the two proteins reconstitutes thefunctional activator protein and results in expression of the reportergene, which is detected by an assay for the reporter gene product.

The two-hybrid system or related methodology can be used to screenactivation domain libraries for proteins that interact with a hostprotein involved in viral infection. Total genomic or cDNA sequences arefused to the DNA encoding an activation domain. This library and aplasmid encoding a hybrid of the host protein involved in viralinfection fused to the DNA-binding domain are cotransformed into a yeastreporter strain, and the resulting transformants are screened for thosethat express the reporter gene. These colonies are purified and theplasmids responsible for reporter gene expression are isolated. DNAsequencing is then used to identify the proteins encoded by the libraryplasmids.

For example, and not by way of limitation, a host gene encoding aprotein involved in viral infection (such as those listed in Table 1 andtarget sequences associated with SEQ ID NOS: 1-232) can be cloned into avector such that it is translationally fused to the DNA encoding theDNA-binding domain of the GAL4 protein. A cDNA library of the cell linefrom which proteins that interact with the host protein are to bedetected can be made using methods routinely practiced in the art. Inthis particular system, the cDNA fragments can be inserted into a vectorsuch that they are translationally fused to the activation domain ofGAL4. This library can be co-transformed along with the host-GAL4 DNAbinding domain fusion plasmid into a yeast strain which contains a lacZgene driven by a promoter which contains GAL4 activation sequences. AcDNA encoded protein, fused to GAL4 activation domain, that interactswith the host protein will reconstitute an active GAL4 protein andthereby drive expression of the lacZ gene. Colonies which express lacZcan be detected by their blue color in the presence of X-gal. The cDNAcan then be extracted from strains derived from these and used toproduce and isolate the host protein-interacting protein usingtechniques routinely practiced in the art.

EXAMPLE 12 Rapid Screening Assays

Prior to performing any assays to detect interference with theassociation of a host protein involved in viral infection and a viralprotein such as an HIV, Ebola, or influenza A protein, rapid screeningassays can be used to screen a large number of agents to determine ifthey bind to the host or viral protein. Rapid screening assays fordetecting binding to HIV proteins have been disclosed, for example inU.S. Pat. No. 5,230,998, which is incorporated by reference. In thatassay, a host protein (such as those listed in Table 1 and targetprotein sequences associated with SEQ ID NOS: 1-232) or a viral protein,such as an HIV protein, is incubated with a first antibody capable ofbinding to the host or viral protein, and the agent to be screened.Excess unbound first antibody is washed and removed, and antibody boundto the host or viral protein is detected by adding a second labeledantibody which binds the first antibody. Excess unbound second antibodyis then removed, and the amount of the label is quantitated. The effectof the binding effect is then determined in percentages by the formula:(quantity of the label in the absence of the test agent)−(quantity ofthe label in the presence of the test agent/quantity of the label in theabsence of the test agent)×100.

Agents that are found to have a high binding affinity to the host orviral protein can then be used in other assays more specificallydesigned to test inhibition of the host protein/viral proteininteraction, or inhibition of viral replication.

EXAMPLE 13 Assays for Measuring Inhibition of Viral Infection

Any of the test agents identified in the foregoing assay systems can betested for their ability to decrease or inhibit infection by a pathogenor virus such as HIV, Ebola, or influenza A.

Cell-Based Assays

Exemplary methods are provided in Example 3 above. Briefly, cells(20,000 to 250,000) are infected with the desired pathogen, such as HIV,Ebola, or influenza A, and the incubation continued for 3-7 days. Thetest agent can be applied to the cells before, during, or afterinfection with the virus. The amount of virus and agent administered canbe determined by skilled practitioners. In some examples, severaldifferent doses of the potential therapeutic agent can be administered,to identify optimal dose ranges. Following transfection, assays areconducted to determine the resistance of the cells to infection byvarious agents.

For example, the presence of a viral antigen can be determined by usingantibody specific for the viral protein then detecting the antibody. Inone example, the antibody that specifically binds to the viral proteinis labeled, for example with a detectable marker such as a flurophore.In another example, the antibody is detected by using a secondaryantibody containing a label. The presence of bound antibody is thendetected, for example using microscopy, flow cytometry, and ELISA.

Alternatively or in addition, the ability of the cells to survive viralinfection is determined, for example by performing a cell viabilityassay, such as trypan blue exclusion.

Animal Model Assays

The ability of an agent, such as those identified using the methodsprovide above, to prevent or decrease infection by a virus, such as HIV,Ebola, or influenza A, can be assessed in animal models. Several animalmodels for viral infection are known in the art. For example, mouse HIVmodels are disclosed in Sutton et al. (Res. Initiat Treat. Action,8:22-4, 2003) and Pincus et al. (AIDS Res. Hum. Retroviruses 19:901-8,2003); guinea pig models for Ebola infection are disclosed in Parren etal. (J. Virol. 76:6408-12, 2002) and Xu et al. (Nat. Med. 4:37-42,1998); and cynomolgus monkey (Macaca fascicularis) models for influenzainfection are disclosed in Kuiken et al. (Vet. Pathol. 40:304-10, 2003).Such animal models can also be used to test agents for an ability toameliorate symptoms associated with viral infection. In addition, suchanimal models can be used to determine the LD50 and the ED50 in animalsubjects, and such data can be used to determine the in veto efficacy ofpotential agents.

Animals of any species, including, but not limited to, mice, rats,rabbits, guinea pigs, pigs, micro-pigs, goats, and non-human primates,such as baboons, monkeys, and chimpanzees, can be used to generate ananimal model of viral infection if needed.

The appropriate animal is inoculated with the desired virus, in thepresence or absence of the test agents identified in the examples above.The amount of virus and agent administered can be determined by skilledpractitioners. In some examples, several different doses of thepotential therapeutic agent can be administered to different testsubjects, to identify optimal dose ranges. The therapeutic agent can beadministered before, during, or after infection with the virus.Subsequent to the treatment, animals are observed for the development ofthe appropriate viral infection and symptoms associated therewith. Adecrease in the development of the appropriate viral infection, orsymptoms associated therewith, in the presence of the test agentprovides evidence that the test agent is a therapeutic agent that can beused to decrease or even inhibit viral infection in a subject.

Having illustrated and described the principles of the invention byseveral examples, it should be apparent that those embodiments can bemodified in arrangement and detail without departing from the principlesof the invention. Thus, the invention includes all such embodiments andvariations thereof, and their equivalents.

1. A method of decreasing infection of a host cell by a virus,comprising interfering with an activity or expression of one or morehost proteins or interfering with an activity of one or more hostnucleic acids, wherein the host protein or host nucleic acid is a T-cellreceptor V beta chain; T-cell receptor V-D-J beta 2.1 chain; β-chimerin;malic enzyme 1; hypothetical protein XP_(—)174419; sequence fromchromosome 4q31.3-32; alpha satellite DNA; LOC253788; LOC219938;coagulation factor III (F3); LOC91759; similar to KOX4 (LOC131880);LOC166140; LOC222474; similar to Rho guanine nucleotide exchange factor4, isoform a; APC-stimulated guanine nucleotide exchange factor(LOC221178); T-cell receptor beta; ribosomal protein L7A-like 4; v-srcsarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) (SRC);KIAA0564; alpha satellite DNA; M96 protein; hypothetical protein similarto G proteins (LOC57826); LOC161005; osteoblast specific factor 2; Canisfamiliaris T-cell leukemia translocation-associated protein;aminomethyltransferase; dystroglycan; bassoon; LIM domain containingpreferred translocation partner in lipoma; sequence between LOC253121and hyaluronan synthase 2; testin 2, testin 3; protein tyrosinephosphatase, non-receptor type 1; sequence between LOC149360 andLOC253961; sequence between KIAA1560 and tectorin beta; cadherin related23; myeloid/lymphoma or mixed lineage leukemia, translocated to 10;exportin 5; DNA polymerase eta (POLH); heterogenous nuclear riboproteinC (C1/C2); alpha-endosulfine pseudogene; LOC128741; LOC222888;LOC138421; zinc finger protein 297B; sideroflexin 5; importin 9(FLJ10402); T-cell receptor beta; similar to murine putativetranscription factor ZNF131 (LOC135952); KIAA1259; MURR1; CCT4;FLJ40773; similar to ribosomal protein L24-like (LOC149360); polybromo1; DNA damage inducible transcript 3; KIAA1887; PDZ; LIM domain 1(elfin); LOC284803; PRO0097; FLJ31958; small inducible cytokine E,member 1 (endothelial monocyte-activating); E3 ubiquitin ligase(SMURF2); MGC40489; Rab9; PRO1617; retinoblastoma binding protein 1;region of chromosome 2q12; elongation factor for selenoproteintranslation; Transcription factor SMIF (HSA275986); KIAA1026;trinucleotide repeat containing 5 (TNRC5); homogentisate 1,2-dioxygenase(HGD); region of chromosome Xq23-24; region of chromosome 4p15.3;similar to LWamide neuropeptide precursor protein [Hydractinia echinata](LOC129883); region of chromosome 2q21; region of chromosome Xp11.4,including UPS9X; LOC221829; U3 small nuclear RNA; integrin, beta 1(ITGB1); acrosomal vesicle protein 1 (ACRV1) and CHK1 checkpoint homolog(CHEK1); prospero-related homeobox 1 (PROX1); FLJ20627 and FLJ12910;PIN2-interacting protein (PINX1) and SRY (sex-determining region Y)-box7 (SOX7); LOC131920; region of chromosome 13q14; neurotrophic tyrosinekinase, receptor, type 3 (NTRK3); TERA protein and FLJ13224; LOC284260;POM (POM121 homolog) and ZP3 fusion (POMZP3); DEAD/H box polypeptide 8(DDX8) and similar to ribosomal protein L29 (cell surface heparinbinding protein HIP) (LOC284064); LOC345307 andUDP-N-acetyl-D-galactosamine:polypeptideN-acetylgalactosaminyltransferase 7 (GALNT7); Mus musculus 5S rRNApseudogene (Rn5s-ps1); ribosomal protein L27a pseudogene (RPL27AP) andv-myb myeloblastosis viral oncogene homolog-like 2 (MYBL2); Down'ssyndrome cell adhesion molecule like 1 (DSCAML1); LOC148529;Huntingtin-associated protein interacting protein (HAPIP); LOC158525 andsimilar to RIKEN cDNA 1210001E11 (LOC347366); hypothetical proteinFLJ12910; LOC350411; allograft inflammatory factor 1 (AIF1) and HLA-Bassociated transcript 2 (BAT2); C10orf7; LOC346658 and LOC340349; regionof chromosome 12q21; LOC339248 and FLJ22659; SR rich proteinDKFZp564B0769 and hypothetical protein MGC14793; FLJ10439; cytochromeP450, family 11, subfamily A, polypeptide 1 (CYP11A1) and sema domain,immunoglobulin domain (Ig) and GPI membrane anchor, (semaphoring) 7A;ribosomal protein S16 (RPS16); hypothetical protein DKFZp434H0115 andATP citrate lyase (ACLY); calnexin (CANX); protein tyrosine phosphatase,receptor type, K (PTPRK); cyclin M2 (CNNM2); or AXL receptor tyrosinekinase (AXL), and wherein interfering with the activity or expression ofthe one or more host proteins decreases infection of the host cell bythe virus.
 2. The method of claim 1, wherein the one or more hostproteins is encoded by one or more host nucleic acids comprising atleast 90% identity to any target nucleic acid sequence associated withSEQ ID NOS: 1-227, 229 or
 231. 3. The method of claim 2, wherein the oneor more host nucleic acids comprises any target nucleic acid sequenceassociated with SEQ ID NOS: 1-227, 229 or
 231. 4. The method of claim 1,wherein the method comprises interfering with an activity or expressionof more than one of the host proteins.
 5. The method of claim 1, whereinthe method comprises interfering with an activity or expression of atleast three of the host proteins.
 6. The method of claim 1 wherein thevirus is HIV-1 or HIV-2, and the host protein or host nucleic acid is aT-cell receptor V beta chain; T-cell receptor V-D-J beta 2.1 chain;β-chimerin; malic enzyme 1; hypothetical protein XYP_(—)174419; sequencefrom chromosome 4q31.3-32; alpha satellite DNA; LOC253788; LOC219938;coagulation factor III; LOC91759; similar to KOX4 (LOC131880);LOC166140; LOC222474; similar to Rho guanine nucleotide exchange factor4, isoform a; APC-stimulated guanine nucleotide exchange factor(LOC221178); T-cell receptor beta; ribosomal protein L7A-like 4(RPL7AL4); v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog(avian) (SRC); KIAA0564; alpha satellite DNA; M96 protein; hypotheticalprotein similar to G proteins; RAP-2A (LOC57826); LOC161005; Rab9, orosteoblast specific factor
 2. 7.-8. (canceled)
 9. The method of claim 1wherein the virus is influenza A, and the host protein is a Canisfamiliaris T-cell leukemia translocation-associated protein,aminomethyltransferase; dystroglycan; bassoon; LIM domain containingpreferred translocation partner in lipoma; sequence between LOC253121and hyaluronan synthase 2; testin 2; testin 3; PTPN1 gene for proteintyrosine phosphatase, non-receptor type 1; sequence between LOC149360and LOC253961; sequence between KIAA1560 and tectorin beta; cadherinrelated 23; malic enzyme 1; hypothetical protein XP_(—)174419; sequencefrom chromosome 4q31.3-32; Rab9, or a myeloid/lymphoma or mixed lineageleukemia, translocated to
 10. 10.-11. (canceled)
 12. The method of claim1 wherein the virus is Ebola, and the host protein is a exportin 5; DNApolymerase eta (POLH); heterogenous nuclear riboprotein C;alpha-endosulfine pseudogene; LOC128741; LOC222888; LOC138421; zincfinger protein 297B; sideroflexin 5; importin 9 (FLJ10402); T-cellreceptor beta; similar to murine putative transcription factor ZNF131(LOC135952); KIAA1259; MURR1; CCT4; FLJ40773; ribosomal protein L24-like(LOC149360); testin 2; testin 3; polybromo 1; DNA damage inducibletranscript 3; KIAA1887; PDZ; LIM domain 1 (elfin); LOC284803; PRO0097;FLJ31958; small inducible cytokine E, member 1 (endothelialmonocyte-activating); E3 ubiquitin ligase; MGC40489; Rab9; PRO1617;retinoblastoma binding protein 1; region of chromosome 2q12; elongationfactor for selenoprotein translation; Transcription factor SMIF(HSA275986); KIAA1026; trinucleotide repeat containing 5 (TNRC5);homogentisate 1,2-dioxygenase (HGD); region of chromosome Xq23-24;region of chromosome 4p 15.3; similar to LWamide neuropeptide precursorprotein [Hydractinia echinata] (LOC129883); region of chromosome 2q21;region of chromosome Xp11.4, including UPS9X; LOC221829; U3 smallnuclear RNA; integrin, beta 1 (ITGB1); acrosomal vesicle protein 1(ACRV1) and CHK1 checkpoint homolog (CHEK1); prospero-related homeobox 1(PROX1); FLJ20627 and FLJ12910; PIN2-interacting protein (PINX1) and SRY(sex-determining region Y)-box 7 (SOX7); LOC131920; region of chromosome13q14; neurotrophic tyrosine kinase, receptor, type 3 (NTRK3); TERAprotein and FLJ13224; LOC284260; POM (POM121 homolog) and ZP3 fusion(POMZP3); DEAD/H box polypeptide 8 (DDX8) and similar to ribosomalprotein L29 (cell surface heparin binding protein HIP) (LOC284064);LOC345307 and UDP-N-acetyl-D-galactosamine:polypeptideN-acetylgalactosaminyltransferase 7 (GALNT7); Mus musculus 5S rRNApseudogene (Rn5s-ps1); ribosomal protein L27a pseudogene (RPL27AP) andv-myb myeloblastosis viral oncogene homolog-like 2 (MYBL2); Down'ssyndrome cell adhesion molecule like 1 (DSCAML1); LOC148529;Huntingtin-associated protein interacting protein (HAPIP); LOC158525 andsimilar to RIKEN cDNA 1210001E11 (LOC347366); hypothetical proteinFLJ12910; LOC350411; allograft inflammatory factor 1 (AIF1) and HLA-Bassociated transcript 2 (BAT2); C10orf7; LOC346658 and LOC340349; regionof chromosome 12q21; LOC339248 and FLJ22659; SR rich proteinDKFZp564B0769 and hypothetical protein MGC14793; FLJ10439; cytochromeP450, family 11, subfamily A, polypeptide 1 (CYP11A1) and sema domain,immunoglobulin domain (Ig) and GPI membrane anchor, (semaphoring) 7A;ribosomal protein S16 (RPS16); hypothetical protein DKFZp434H0115 andATP citrate lyase (ACLY); calnexin (CANX); protein tyrosine phosphatase,receptor type, K (PTPRK); cyclin M2 (CNNM2); or AXL receptor tyrosinekinase. 13.-14. (canceled)
 15. The method of claim 6, wherein the one ormore host proteins are encoded by one or more nucleic acid sequencescomprising at least 90% identity to any target nucleic acid sequenceassociated with SEQ ID NOS: 1-35.
 16. The method of claim 6, wherein oneor more host proteins is encoded by one or more nucleic acid sequencescomprising any target nucleic acid sequence associated with SEQ ID NOS:1-35.
 17. The method of claim 9, wherein the one or more host proteinsare encoded by one or more nucleic acid sequences comprising at least90% identity to any of SEQ ID NOS: 36-63 or a coding sequence of any ofSEQ ID NOS: 36-63.
 18. The method of claim 9, wherein the one or morehost proteins are encoded by one or more nucleic acid sequencescomprising any target nucleic acid sequence associated with SEQ ID NOS:36-63.
 19. The method of claim 12, wherein the one or more host proteinsare encoded by one or more nucleic acid sequences comprising at least90% identity to any target nucleic acid sequence associated with SEQ IDNOS: 64-227, 229, and
 231. 20. The method of claim 12, wherein one ormore host proteins are encoded by one or more nucleic acid sequencescomprising any target nucleic acid sequence associated with SEQ ID NOS:64-227, 229, and
 231. 21. The method of claim 1, wherein interferingwith the activity of the one or more host proteins comprises decreasingan interaction of a viral protein and the one or more host proteins bydisrupting or decreasing expression of the one or more host proteins.22. The method of claim 21, wherein the viral protein comprises a virusand decreasing the interaction of the viral protein and the one or morehost proteins decreases or inhibits infection of a host cell by thevirus.
 23. The method of claim 21, wherein disrupting or decreasingexpression of the host protein comprises disrupting or decreasingtranscription of an mRNA encoding the host protein.
 24. The method ofclaim 23, wherein disrupting or decreasing transcription of the mRNAcomprises inserting a transposon or insertional vector into a codingregion of the nucleic acid encoding the host protein.
 25. The method ofclaim 23, wherein disrupting or decreasing the transcription of the mRNAcomprises contacting the mRNA with an antisense RNA, RNAi, ribozyme, orsiRNA that recognizes the mRNA.
 26. The method of claim 1 whereininterfering with the activity of the host protein comprises decreasingan interaction of a viral protein and the host protein by contacting thecell with an agent that decreases or inhibits the activity or expressionof the host protein or that disrupts expression of the host protein. 27.The method of claim 26, wherein the host cell is present in a hostsubject and wherein contacting the cell with the agent comprisesadministering the agent to the subject.
 28. The method of claim 1,wherein the host cell is a mammalian host cell.
 29. A method ofdecreasing HIV, Ebola, or influenza A infection of a host cell,comprising, decreasing an interaction between a viral nucleic acid and ahost nucleic acid by decreasing the integration of the viral nucleicacid into the host nucleic acid, wherein the host nucleic acid comprisesat least 90% identity to any target sequence associated with SEQ ID NOS:1-227, 229, and
 231. 30. The method of claim 29, wherein the viralnucleic acid comprises a viral genome and the host nucleic acidcomprises a host genome.
 31. A method of treating an HIV, Ebola, orinfluenza A viral infection in a host subject, comprising administeringto a subject having a viral infection an effective amount of an agentthat interferes with the interaction of a virus and host protein,wherein the host protein is encoded by a nucleic acid comprising atleast 90% identity to any target sequence associated with SEQ ID NOS:1-227, 229, and
 231. 32. The method of claim 31, wherein the agentdisrupts expression of the nucleic acid encoding the host protein. 33.The method of claim 32, wherein the agent is an antisense, ribozyme, orsiRNA molecule that recognizes the nucleic acid sequence comprising atleast 90% identity to any target sequence associated with SEQ ID NOS:1-227, 229, and
 231. 34. The method of claim 31, wherein the effectiveamount induces a prophylactic effect in the host, which inhibitsinfection of the host by a virus.
 35. The method of claim 31, whereinthe host was previously infected by a virus and the effective amountinduces a therapeutic effect in the host.
 36. A method of determiningresistance or susceptibility to viral infection in a subject, comprisingcomparing a first nucleic acid sequence of a subject to a second nucleicacid sequence comprising any target sequence associated with SEQ ID NOS:1-227, 229, and 231, wherein a higher similarity between the first andsecond nucleic acid sequence indicates the subject is more susceptibleto viral infection, and wherein a lesser similarity between the firstand second nucleic acid sequence indicates the subject is more resistantto viral infection.
 37. The method of claim 36, wherein the firstnucleic acid sequence is obtained from a biological sample of thesubject.
 38. The method of claim 37, wherein the first nucleic acidsequence comprises a plurality of nucleic acid sequences, wherein eachnucleic acid sequence is obtained from a different subject.
 39. Themethod according to claim 36, further comprising determining apolymorphic variation within a population.
 40. A method of decreasingHIV, Ebola, or influenza A infection of a host cell, comprising:contacting the host cell with an anti-protein binding agent thatselectively or specifically binds to a host protein encoded by anytarget sequence associated with SEQ ID NOS: 1-227, 229, and 231 or aprotein sequence shown in any of SEQ ID NOS: 228, 230, or 232, whereinthe anti-protein binding agent inhibits an interaction between the hostprotein and the HIV, Ebola, or influenza A virus.
 41. The method ofclaim 40, wherein the host cell is present in a subject, and contactingthe host cell with the anti-protein binding agent comprisesadministering the anti-protein binding agent to the subject. 42.(canceled)
 43. A method of identifying a compound that decreases bindingof a viral protein to a host protein and decreases viral infection,comprising: contacting the host protein with the viral protein and atest compound, wherein the host protein is a protein in Table 1, and theviral protein is an HIV, Ebola, or influenza A protein; and determiningwhether binding of the viral protein to the host protein is decreased inthe presence of the test compound, the decrease in binding being anindication that the test compound decreases the binding of viral proteinto the target protein, and decreases viral infection.
 44. The method ofclaim 43, wherein the viral protein comprises a virus.
 45. The method ofclaim 43, wherein the viral protein is a viral envelope protein.
 46. Themethod of claim 43, wherein the viral protein is an HIV protein and thehost protein is a protein encoded by a target sequence associated withSEQ ID NOS: 1-35.
 47. The method of 43, wherein the viral protein is aninfluenza A protein and the host protein is a protein encoded by atarget sequence associated with SEQ ID NOS: 36-63.
 48. The method ofclaim 43, wherein the viral protein is an Ebola protein and the hostprotein is a protein encoded by a target sequence associated with SEQ IDNOS: 64-227, 229, and
 231. 49. The method of claim 43, wherein themethod comprises expressing the host protein in a cell, and contactingthe host protein with the viral protein and a test compound comprisesexposing the cell to the viral protein and the test compound.
 50. Themethod of claim 43, wherein the host protein or the viral proteincomprises a label, and determining whether binding is decreasedcomprises detecting an amount of label present.
 51. A method ofdecreasing infection of a host cell by a pathogen, comprisinginterfering with an activity or expression of a Rab9 in the host cell,wherein interfering with Rab9 activity or expression decreases infectionof the host cell by the pathogen.
 52. The method of claim 51, whereinthe pathogen hijacks a lipid raft.
 53. The method of claim 51, whereinthe pathogen is a Campylobacter jujuni, Vibrio cholerae, SV40,Legionella pneumophila, Aeromonas hydrophilia, Echovirus 1, Echovirus11, Brucella spp, Clostridium spp., Avian sarcoma and leukosis virus,FimH, Dr Escherichia coli, Streptcoccus pyogenes, Semiliki forest virus,Salmonella typhimurium, Bacillus anthracis, Ecotropic mouse leukaemiavirus, Shigella flexneri, Bacillus thuringiensis, HTLV-1, Chlamydiaspp., Helicobacter pylori, HIV-1, Mycobacterium spp., Lysteriamonocytogenes, Ebola, Marburg, Measles, Herpes Simplex virus, influenzavirus, or Epstein-Barr virus.
 54. The method of claim 51, wherein theRab9 host protein is encoded by a host nucleic acid comprising at least90% identity to a target sequence associated with any of SEQ ID NOS:118-119.
 55. The method of claim 54, wherein the host nucleic acidcomprises a target sequence associated with any of SEQ ID NOS: 118-119.56. The method of claim 51, wherein interfering with expression of Rab9comprises disrupting or decreasing transcription of an mRNA encoding theRab9 protein.
 57. The method of claim 56 wherein disrupting ordecreasing the transcription of the mRNA comprises contacting the mRNAwith an antisense RNA, ribozyme, or siRNA that recognizes the mRNA. 58.The method of claim 57, wherein the siRNA sequence comprises any of SEQID NOS: 232-235.
 59. The method of claim 57, wherein the host cell ispresent in a subject, and contacting the mRNA with an antisense RNA,ribozyme, or siRNA that recognizes the mRNA comprises administering theantisense RNA, ribozyme, or siRNA to the subject.
 60. A cell comprisinga functional deletion of one or more target sequences associated withany of SEQ ID NOS: 1-35, wherein the cell has a decreased susceptibilityto HIV infections SEQ ID NOS: 36-63, wherein the cell has a decreasedsusceptibility to influenza infection; or SEQ ID NOS: 64-232, whereinthe cell has a decreased susceptibility to Ebola infection. 61.-62.(canceled)
 63. A cell comprising a functional deletion of a Rab9 gene,wherein the cell has a decreased susceptibility to infection by apathogen that uses lipid rafts.
 64. A non-human transgenic mammalcomprising a functional deletion of one or more target sequencesassociated with any of SEQ ID NOS: 1-35, wherein the mammal hasdecreased susceptibility to infection by HIV; SEQ ID NOS: 36-63, whereinthe mammal has decreased susceptibility to infection by influenza; orSEQ ID NOS: 64-232, wherein the mammal has decreased susceptibility toinfection by Ebola. 65.-66. (canceled)
 67. A non-human transgenic mammalcomprising the cell of claim 63, wherein the mammal has decreasedsusceptibility to infection by a pathogen that uses a lipid raft. 68.The method of claim 1, wherein interfering with an activity of the hostnucleic acid comprising administering one or more of SEQ ID NOS: 246-845to the host cell.